title: WT

city: Los Angeles

first: Sai

last: Xiao

address: 1500 E. Duarte Road

institute: City of Hope

data_processing:
Cell Ranger (version 5.0.1) was used to process the raw data, demultiplex cellular barcodes, map reads to the transcriptome, and down-sample reads (as required to generate normalized aggregate data across samples). Genes with less detected cell numbers (less than 3) and cells with less detected genes (less than 200) were removed. Low-quality cells were removed if the number of expressed genes was smaller than 200 or larger than 5000. Cells were also removed if their proportions of mitochondrial gene expression were larger than 7.5%. Finally, 19,530 single cells remained, and they were applied in downstream analyses. To cluster single cells by their expression, the unsupervised graph-based clustering algorithm implemented in Seurat R package (version 4.0.4) was used for each data set. Top 2,500 variable genes identified by vst method were used to perform principal component analysis. 1-30 PCs were used in FindNeighbors function. The FindClusters function was used to determine the clusters (res = 0.7), and then they were visualized with 2D tSNE plots.
Assembly: mm10
Supplementary files format and content: Tab-separated values and matrix files

growth_protocol: WT and Ythdf2-KO tumors from C57BL/6 mice were extracted and digested with collagenase type IV (1 mg/ml) and DNase type I (30 U/ml) for 30 min at 37 °C. The cells were filtered through the 70 μm cell strainers, washed with phosphate-buffered saline (PBS), lysed in red blood cell buffer, and resuspended in PBS. Tumor-infiltrating immune cells (CD45+ cells) were sorted by FACSAria Fusion Flow Cytometer (BD Biosciences).

extract_protocol:
The cell suspension (300-600 living cells per microliter) was loaded onto the Chromium single cell controller (10 x Genomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol.
Libraries were subsequently prepared sing Single Cell 5’Library and Gel Bead Kit and sequenced on an Illumina NovaSeq 6000 instrument with pair-end 100 bp (PE100) reading strategy.

treatment_protocol: Tumor-infiltrating immune cells (CD45+ cells) were purified  from WT or Ythdf2-KO tumors.

value: WT


title: MC38-RIP--1

status: Public on May 31 2024

type: SRA

state: California

country: USA

library_source: transcriptomic

data_processing:
Sequencing reads were mapped to the mouse genome using HISAT2
Mapped reads of IP and input libraries were provided for R package exomePeak
The m6A binding motif was analyzed by HOMER.
Called peaks were annotated by intersection with gene architecture using R package ChIPseeker
Peak calling results with IP and input libraries were generated by exomePeak2
Called peaks were annotated by intersection with gene and transcript architecture using ChIPpeakAnno
Assembly: mm10
Supplementary files format and content: Browser Extensible Data files includes callpeak sites
Supplementary files format and content: comma-separated values files includes count matrix

molecule: total RNA

organism: Mus musculus

source_name: MC38 cell line

growth_protocol: WT and Ythdf2-KO MC38 tumor cells were grew in DMEM (Gibco) supplemented with 10% FBS (Gibco), 1% penicillin/streptomycin (Gibco).

extract_protocol:
For m6A-seq, total RNA was isolated by TRIzol reagent. Polyadenylated RNA was further enriched from total RNA by using Dynabeads® mRNA Purification Kit (Invitrogen). mRNA samples were fragmented into ~100-nucleotide-long fragments with RNA fragmentation reagents (Invitrogen). Fragmented mRNA (5 μg mRNA) was used for m6A immunoprecipitation (m6A-IP) using an m6A antibody (Synaptic, 202003) following the standard protocol of the Magna MeRIP m6A Kit (Merck Millipore). For Ythdf2 RIP-seq, fifty million tumor cells were harvested and washed twice with cold PBS, and the cell pellet was lysed with two volumes of lysis buffer [10 mM HEPES pH 7.6, 150 mM KCl, 2 mM EDTA, 0.5% NP-40, 0.5 mM DTT, 1:100 Protease Inhibitor cocktail (Thermo Fisher Scientific), and 400 U/mL SUPERase-In RNase Inhibitor (Thermo Fisher Scientific)]. The lysate was incubated on ice for 5 min and centrifuged for 15 min to clear the lysate. One-tenth volume of cell lysate was saved as input. The rest of the cell lysate was incubated with 5 μg anti-YTHDF2 (MBL, Cat No. RN123PW) that was pre-coupled with Protein A magnetic beads (Invitrogen, Cat: 10001D) at 4℃ for 2h with gentle rotation. Afterward, the beads were washed five times with 1 ml ice-cold washing buffer (50 mM HEPES pH 7.6, 200 mM NaCl, 2 mM EDTA, 0.05% NP-40, 0.5 mM DTT, and 200 U/mL RNase inhibitor). Immunoprecipitated samples were subjected to Proteinase K digestion in wash buffer supplemented with 1% SDS and 2 mg/mL Proteinase K (Thermo Fisher Scientific) incubated with shaking at 1200 rpm at 55℃ for 1 h. Total RNA was extracted from both input and immunoprecipitated RNA by adding 5 volumes of TRIzol reagent, followed by Direct-zol RNA Miniprep (Zymo Research).
For m6A-seq,RNA was enriched through RNA Clean & Concentration- 5 (Zymo Research) for library generation with a KAPA RNA HyperPrep Kit (Roche). Sequencing was performed at the City of Hope Genomics Facility on an Illumina NovaSeq 6000  machine with 100-bp paired-end reads (PE100). For Ythdf2 RIP-seq, cDNA library generation was produced with a KAPA RNA HyperPrep Kit (Roche) and sequenced on Illumina NovaSeq 6000 platform.

tag: cell line

value: MC38 cell line

tag: genotype


title: pol3090 BrdU 25C 30' MNase rep1 [Alb398_pol3090_BrdU_S30]

city: New York

first: zhiguo

last: zhang

state: NY

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

institute: Columbia University

library_source: genomic

data_processing:
Raw reads were firstly trimmed by Cutadapt (Marcel, 2011) to remove adapters and low quality reads, and then mapped to the yeast genome (sacCer3) using Bowtie2 (Langmead and Salzberg, 2012).Duplicate reads were further filtered by Sambamba (Tarasov et al., 2015) to remove PCR duplication.
The genome-wide read coverage on Watson and Crick strands were calculated at the bin of 1bp using deepTools bamCoverage (Ramirez et al., 2016). Then, the raw genome-wide read coverage was normalized with the number of total mapped reads to obtain counts per million value (CPM).
Spike-in added samples normalization. For each Sonication-BrdU-IP-ssSeq sample, the raw genome-wide coverage was normalized using the formula: BrdUsoni = (BrdUcov / BrdUspike) / (Inputread / Inputspike). BrdUcov is the raw coverage of BrdU-IP-ssSeq; BrdUspike is the number of total mapped spike-in reads (S. pombe reads) in BrdU sample, Inputread is the number of total mapped reads in input, and Inputspike is the number of total mapped spike-in reads (S. pombe) in input. In this way, BrdU incorporation at each strain was quantified as BrdUsoni.
Spike in added samples normalization. For each MNase-BrdU-IP-ssSeq dataset, reads with the nucleosome sized (120~170bp) were first selected to calculate the raw coverage of nucleosome occupancy surrounding replication origins, and then normalized using the formula: BrdUMNase = (BrdUcov-MNase / BrdUspike-MNase) / (Inputread-MNase / Inputspike-MNase). BrdUcov-MNase is the raw coverage of the nucleosome-sized reads, BrdUspike-MNase is the number of mapped nucleosome-sized spike-in reads in the same sample, Inputread-MNase is the number of mapped  nucleosome-sized reads in input, and Inputspike-MNase is the number of mapped nucleosome-sized spike-in reads in the same input sample. In this way, the nucleosome occupancy on nascent chromatin was quantified as BrdUMNase.
Assembly: saccer3
Supplementary files format and content: tar of bw, bigwig format, CPM which is normalized by total number of reads
Supplementary files format and content: tar of bw, bigwig format, BrdU coverage normalized by spike-in and input described as formulas above.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: pol3090 BrdU 25C 30' MNase

growth_protocol: For most experiments, yeast cells were cultured and synchronized at G1 phase following standard procedures (Dunham et al., 2015). ChIP, BrdU-IP-ssSeq, and eSPAN sample collection was performed as described previously (Gan et al., 2017; Yu et al., 2018). Briefly, exponentially growing yeast cultures at OD600=0.4-0.5 were synchronized by adding a-factor at 5mg/ml and arrested for 3h at 25°C.

extract_protocol:
For analysis of DNA replication by BrdU-IP-ssSeq, and PCNA ChIP and eSPAN experiments, chromatin was fragmented by sonication (15 seconds on and 30 seconds off for 10 cycles in a Bioruptor Pico, Diagenode). For analysis of nucleosome occupancy at nascent chromatin, H3K4me3 and H3K56ac ChIP as well as almost all eSPAN experiments except those marked by sonication, chromatin was digested with MNase to map nucleosomes (Wal and Pugh, 2012).
The ssDNA libraries were prepared using the Accel-NGS 1S Plus kit (Cat no. 10096, Swift Bioscience).

treatment_protocol: Cells were then released into fresh YPD medium containing 400mg/ml BrdU without HU for 30 or 40 minutes at 25°C. For experiments using auxin-inducible protein degradation mutant strains, 1mM IAA or the equivalent volume of ethanol was added to the arresting culture (30 minutes before release) and cells were released in YPD medium also containing IAA or ethanol.

tag: batch

tag: strain

tag: condition

value: 25C 30' MNase

tag: treatment

value: BrdU


title: SHAGGY_6259 day 3

city: Memphis

first: Michael

last: Dyer

state: TN

address: 262 Danny Thomas Pl MS 324

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

data_processing:
Trimmed and initial quality control with FastQC.
Aligning and counting with STAR.
Duplicate removal using GATK ‘MarkDuplicates’.
TPM matrices generated using RSEM.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files with raw counts, rpkm and fpkm for each sample
Supplementary files format and content: Tab-delimited text file with all compiled tpm values for all 16 samples.

organism: Homo sapiens

source_name: Mouse-human xenograft

extract_protocol:
Biopsied tissue underwent RNA extraction using Trizol reagent (Invitrogen). Biopsied tissue was manually homogenized in microcentrifuge tubes using a disposable micro-pestle (Fisher Scientific), and solubilized in 800 mcl Trizol. 200 mcl chloroform was added followed by centrifugation to separate  nucleic acids. The aqueous fraction was collected and RNA was precipatated by the addition of 500 mcl isopropanol and 1 mcl glycogen. Precipirate was pelleted by centrifugation, washed with 75% ethanol, and resolubilized in nuclease-free water.
RNA-sequencing libraries were generated from 250 – 1000 ng of input RNA using the TruSeq Total Stranded RNA Library Kit (Illumina).

tag: tissue

value: xenograft tumor

tag: mouse number

value: vincristine+irinotecan

tag: time point_(days)

tag: xenograft model


title: HDL124_Blood_TCRG

city: New York City

first: Joshua

middle: Ian

last: Gray

state: New York

address: 630 168th Street

department: CCTI

data_processing:
Raw data were processed using the standard immunoSEQ Analyzer from Adaptive Biotechnologies Corporation.
Assembly: Third party provider description: "Sequences were not aligned against a reference genome; instead they were aligned and annotated based on our custom pipeline using primers designed to IMGT reference V and J genes. The CDR3 regions were defined as per IMGT beginning with the second conserved cysteine encoded by 3’ portion of V gene segment. IMGT reference: Yousfi Monod, M., Giudicelli, V., Chaume, D. & Lefranc, M. P. IMGT/JunctionAnalysis: the first tool for the analysis of the immunoglobulin and T cell receptor complex V-J and V-D-J JUNCTIONs. Bioinformatics 20, (Suppl 1): i379–i385 (2004).
Supplementary files format and content: Processed data files are in the form of tsv files containing clonal counts, nt and aa sequences, as well as VDJ subtype information

source_name: Blood

extract_protocol:
DNA was isolated from cell pellets using the DNA micro kit (Qiagen) and DNA concentrations were assessed using the NanoDrop (Thermo Scientific).
Other

value: Blood

tag: cell type

value: gd T cells

tag: developmental stage

value: pediatric

tag: age


title: pol31pip H3K56ac_eSPAN 25C 30' MNase rep2 [Alb774_pol31pip_H3K56ac_eSPAN_S30]

source_name: pol31pip H3K56ac_eSPAN 25C 30' MNase


title: HDL124_Blood_TCRAD


title: SHAGGY_6259 day 0


title: Ythdf2 KO

library_source: transcriptomic single cell

source_name: Tumor-infiltrating immune cells (CD45+ cells)

value: Ythdf2 KO


title: pol31pip H3K56ac_eSPAN 25C 30' MNase rep1 [Alb710_pol31_pip_H3K56ac_eSPAN_S]


title: HDL123_Spleen_TCRG

source_name: Spleen

value: Spleen


title: MC38-RIP-input--1


title: BMMCs, Scrambled, 1

city: Bellinzona

first: Cristina

last: Leoni

state: Ticino

address: Via F. Chiesa 5

department: Molecular Immunology

country: Switzerland

institute: Institute for Research in Biomedicine

data_processing:
Quality control of reads was performed using fastqc v.0.11.9 and RSeQC v.4.0.0 and mapped to reference mouse genome build Mus_musculus.GRCm39.107 using HiSat2 v.2.2.1.
Gene expression counts were generated using featureCounts v.2.0.1 and corrected for batch effect using the removeBatchEffect function in R.
Differential expression analysis was performed using the Omics Playground platform.
Assembly: GRCm39
Supplementary files format and content: *.gene.counts.txt files contain raq read counts for each samples.

source_name: BMMCs

growth_protocol: Total bone marrow was isolated from mouse and cultured in humidified atmosphere with 5% CO2 at 37C for at least 4 weeks in the presence of IL-3 to induce bone marrow-derived mast cell (BMMC) differentiation. BMMCs were transfected with either Zc3h12a or scrambled gRNA-Cas9 RNPs and cultured for 1 week.

extract_protocol:
Cells were resuspended in Trizol and total RNA was extracted with Direct-Zol RNA mini Prep (Zymo Research)
RNA libraries for RNA-seq were prepared using Tecan Revelo mRNA Library Prep Kit following manufacturer's protocols.

value: BMMCs

value: Zc3h12a WT


title: SHAGGY_6260 day 32

value: recurrence


title: pol31pip H3K4me3_eSPAN 25C 30' MNase rep2 [Alb773_pol31pip_H3K4me3_eSPAN_S30]

source_name: pol31pip H3K4me3_eSPAN 25C 30' MNase


title: SHAGGY_6260 day 21


title: HDL123_Spleen_TCRAD


title: pol31pip H3K4me3_eSPAN 25C 30' MNase rep1 [Alb709_pol31_pip_H3K4me3_eSPAN_S]


title: MC38_gY2_Input_3


title: MC38_gY2_Input_2


title: HDL123_Lung_TCRG

source_name: Lung

value: Lung


title: SHAGGY_6260 day 14


title: SHAGGY_6259 day 7


title: MC38-RIP--2


title: MC38_gY2_Input_1


title: pol31pip BrdU 25C 30' MNase rep2 [Alb772_pol31pip_BrdU_S30]

source_name: pol31pip BrdU 25C 30' MNase


title: HDL123_Lung_TCRAD


title: SHAGGY_6260 day 7


title: MC38-RIP-input--2


title: MC38_gNC_Input_3


title: pol31pip BrdU 25C 30' MNase rep1 [Alb708_pol31_pip_BrdU_S]


title: HDL123_LLN_TCRG

source_name: LLN

value: LLN


title: pol32D PCNA_eSPAN 25C 30' sonication rep2 [Alb649_pol32D_PCNA_eSPAN_S30]

source_name: pol32D PCNA_eSPAN 25C 30' sonication

value: 25C 30' sonication


title: HDL123_LLN_TCRAD


title: MC38_gNC_Input_2

value: WT


title: SHAGGY_6260 day 3


title: Patient 17 mid-treatment

data_processing:
Trimming and quality control using FastQC
Aligning and counting STAR.
Duplicate reads were removed using GATK ‘MarkDuplicates’
Count matrices were generated using RSEM ‘rsem-calculate-expression’
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files with raw counts, rpkm and fpkm for each sample
Supplementary files format and content: Tab-delimited text file with all compiled tpm values for all 18 samples.

source_name: rhabdomyosarcoma tumor

extract_protocol:
RNA was extracted using the Maxwell RSC RNA FFPE kit.
Libraries were constructed using the Takara SMARTer Total RNA Pico v2 kit with 10 ng of input FFPE RNA/

value: rhabdomyosarcoma tumor

tag: pax-foxo1 fusion_status

value: negative


title: pol32D PCNA_ChIP 25C 30' sonication rep2 [Alb647_pol32D_PCNA_ChIP_S30]

source_name: pol32D PCNA_ChIP 25C 30' sonication


title: SHAGGY_6260 day 0


title: MC38_gNC_Input_1

value: MC38 cell line


title: MC38_gY2_MeRIP_3


title: HDL116_MLN_TCRAD

source_name: MLN

value: MLN


title: pol32D PCNA_ChIP 25C 30' sonication rep1 [Alb612_pol32D_PCNA_ChIP_S30]


title: HDL116_MLN_TCRG


title: Patient 25 mid-treatment


title: HDL116_Lung_TCRG


title: HDL124_MLN_TCRAD


title: pol32D H3K56ac_eSPAN 25C 30' sonication rep2 [Alb563_pol32D_H3K56ac_eSPAN_S30]

source_name: pol32D H3K56ac_eSPAN 25C 30' sonication


title: MC38_gY2_MeRIP_2

source_name: MC38 cell line


title: MC38_gY2_MeRIP_1


title: Patient 19 mid-treatment

value: positive


title: Patient 12 mid-treatment


title: pol32D H3K56ac_eSPAN 25C 30' sonication rep1 [Alb384_pol32D_H3K56ac_eSPAN_S30]


title: HDL116_LLN_TCRG


title: MC38_gNC_MeRIP_2


title: MC38_gNC_MeRIP_3


title: pol32D H3K4me3_eSPAN 25C 30' sonication rep2 [Alb562_pol32D_H3K4me3_eSPAN_S30]

source_name: pol32D H3K4me3_eSPAN 25C 30' sonication


title: Patient 21 mid-treatment


title: pol32D PCNA_eSPAN 25C 30' sonication rep1 [Alb614_pol32D_PCNA_eSPAN_S30]


title: Patient 24 mid-treatment


title: pol32D H3K4me3_eSPAN 25C 30' sonication rep1 [Alb383_pol32D_H3K4me3_eSPAN_S30]


title: HDL116_LLN_TCRAD


title: MC38_gNC_MeRIP_1


title: HDL115_Spleen_TCRG


title: E12.5, cochlea, replicate 2, snRNA-seq of multiome, 2nd sequencing

city: Augusta

first: Lin

last: Gan

state: Geogia

address: 1120 15th Street

department: Department of Neuroscience & Regenerative Medicine

institute: Augusta University

description: 10x Genomics

data_processing:
Sequences were aligned to the Ensembl mouse mm10 assembly using CellRanger-ARC-2.0.0 (10X Genomics) analysis software
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Cochlea

extract_protocol:
After separating and collecting the cochlea of E12.5, nuclei were isolated according to 10X Genomics protocols (CG000375 Rev C) without FASC sorting.
The libraries for Chromium Single Cell Multiome ATAC + Gene Expression were produced exactly as written (10X Genomics, CG000338 Rev A).

value: Cochlea


title: pol32D BrdU 25C 30' sonication rep4 [Alb648_pol32D_BrdU_S30]

source_name: pol32D BrdU 25C 30' sonication

value: BrdU


title: Patient 2 pre-treatment


title: HDL115_Spleen_TCRAD

value: gd T cells

value: pediatric


title: E12.5, cochlea, replicate 2, snRNA-seq of multiome, 1st sequencing

description: 10x Genomics


title: HDL115_MLN_TCRG


title: Patient 25 pre-treatment


title: HDL115_MLN_TCRAD


title: HDL116_Lung_TCRAD


title: Patient 24 pre-treatment


title: E12.5, cochlea, replicate 2, snATAC-seq of multiome

description: 10x Genomics


title: Patient 21 pre-treatment


title: pol32D BrdU 25C 30' sonication rep1 [Alb382_pol32D_BrdU_S30]


title: HDL115_Lung_TCRG


title: Patient 19 pre-treatment


title: pol32D H3K56ac_eSPAN 25C 30' MNase rep4 [Alb790_pol32D_H3K56ac_eSPAN_S30]

source_name: pol32D H3K56ac_eSPAN 25C 30' MNase

value: 25C 30' MNase


title: HDL115_Lung_TCRAD


title: Patient 17 pre-treatment


title: HDL115_LLN_TCRG


title: pol32D H3K56ac_eSPAN 25C 30' MNase rep3 [Alb782_pol32D_H3K56ac_eSPAN_S30]


title: Patient 12 pre-treatment


title: pol32D H3K56ac_eSPAN 25C 30' MNase rep2 [Alb238_pol32D_H3K56ac_eSPAN_S30]


title: pol32D BrdU 25C 30' sonication rep3 [Alb613_pol32D_BrdU_S30]


title: pol32D H3K56ac_eSPAN 25C 30' MNase rep1 [Alb116_pol32_H3K56ac_eSPAN_S30]


title: Patient 8 mid-treatment


title: A673.EdA.ITP

city: Heidelberg

first: Thomas

middle: Georg Philipp

last: Grunewald

address: Im Neuenheimer Feld 280

department: Division of Translational Pediatric Sarcoma Research

country: Germany

institute: German Cancer Research Center (DKFZ)

description:
batch_1
A673.EdA.ITP

data_processing:
Drop-seq pipeline (v1.0)
picard-2.18.26
STAR-2.6.1
Bcl2Fastq
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include count values for each sample

growth_protocol: All cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and and 1% penicillin-streptomycin in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was isolated using the NucleoSpin RNA kit. 50–100 ng of RNA in three biological and two technical replicates was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared as described in Parekh et al., 2016.

treatment_protocol: no treatment

value: human EwS cell


title: pol32D BrdU 25C 30' sonication rep2 [Alb561_pol32D_BrdU_S30]


title: Patient 8 pre-treatment


title: m148, IgG

first: Spyros

last: Karaiskos

department: Herbert Irving Cancer Center

data_processing:
Reads were aligned to the mouse reference genome mm10 using Bowtie v2.2.8 with parameters -q -I 50 -X 700 --very-sensitive-local --local --no-mixed --no-unal --no-discordant, and reads quality was assessed using fastQC.
Duplicate reads were removed with PICARD v2.2.4 (Broad Institute). Binary alignment maps (BAM) files were generated with samtools v1.9 and were used in downstream analysis. MACS2 v2.1.0 was used to called significant peaks (Peaks within ENCODE blacklisted regions were removed.
Coverage tracks were generated from BAM files using deepTools 3.2.1 bamCoverage with parameters –normalizeUsing RPKM –binsize 10.
For p53-R172H and wild-type p53 ESCC cell lines H3K27ac CUT&RUN-seq, the BAM files were merged in a single BAM and significant peaks were called using MACS2 narrowPeak 2.1.0 to generate a bed file with a common set of regions.
Following, BedTools multicov was used to report the count of alignments from the two samples BAMs at the common set of regions. Differential regions were called if the log2 fold change was greater than |1.5|.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&RUN-Seq

growth_protocol: The cells were cultured in keratinocyte serum-free media, supplemented with 50μg/mL bovine pituitary extract, 5ng/mL human recombinant EGF, 0.018mM CaCl2, and 1% penicillin/streptomycin (KSFM; Gibco #37010022).Cells were cultured at 37C at 5% CO2.

extract_protocol:
3.0x105 ESCC tumor cells per condition were harvested and lightly crosslinked with 0.1% Formaldehyde/PBS solution (Thermo Fisher 28908) for 1 minute at room temperature. The cells bound to activated Biomag Plus Concavalin A beads (Bangs Laboratories, BP531) were incubated with primary antibodies for IgG or H3K27ac on nutator overnight at 4ºC . After binding of pAG-MNase (EpiCypher, 15-1016), the targeted chromatin was digested with 100mM CaCl2 for 30 minutes at 0ºC and the DNA was isolated with phenol-chloroform extraction.
The library prep on the purified DNA was conducted with NEBNext Ultra II DNA Library Prep Kit for Illumina (BioLabs, E7103) following the manufacturer’s suggestions.

value: Esophageal squamous cell carcinoma cells with wild-type p53

tag: chip antibody

value: IgG antibody (Epicypher, #13-0042)

value: wild-type p53


title: HDL115_Jejunum_TCRAD

source_name: Jejunum

value: Jejunum


title: E12.5, cochlea, replicate 1, snRNA-seq of multiome, 2nd sequencing

description: 10x Genomics


title: pol32D H3K4me3_eSPAN 25C 30' MNase rep3 [Alb781_pol32D_H3K4me3_eSPAN_S30]

source_name: pol32D H3K4me3_eSPAN 25C 30' MNase


title: HDL111_Spleen_TCRG

source_name: Spleen

value: Spleen


title: HDL115_LLN_TCRAD

value: LLN


title: HDL111_Spleen_TCRAD


title: m20, H3K27ac

value: Esophageal squamous cell carcinoma cells with p53-R172H mutation

value: H3K27ac antibody (CST, #8173)


title: E12.5, cochlea, replicate 1, snRNA-seq of multiome, 1st sequencing

description: 10x Genomics


title: m20, IgG


title: Patient 5 pre-treatment

value: rhabdomyosarcoma tumor

value: negative


title: pol32D H3K4me3_eSPAN 25C 30' MNase rep4 [Alb789_pol32D_H3K4me3_eSPAN_S30]


title: m139, H3K27ac, biol rep 2


title: HDL111_MLN_TCRG

value: MLN


title: E12.5, cochlea, replicate 1, snATAC-seq of multiome

description: 10x Genomics

value: Cochlea


title: Patient 5 mid-treatment


title: Patient 2 mid-treatment


title: pol32D H3K4me3_eSPAN 25C 30' MNase rep1 [Alb115_pol32_H3K4me3_eSPAN_S30]


title: HDL111_MLN_TCRAD


title: m148, H3K27ac


title: NALM-6 cells, shHBO1, rep3

city: Guangzhou

first: Ning

last: Chang

address: 253 Industrial Avenue

country: China

institute: Zhujiang Hospital, Southern Medical University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Hisat2 tools soft were used to map with reference genome.
Quantification of gene expression was used StringTie
Differential expression analysis  was performed using the DESeq2.
Assembly: GRCh38
Supplementary files format and content: TXT files include FPKM and count values for each Sample

source_name: Peripheral blood

growth_protocol: NALM-6 cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum(FBS) at 37℃ with 5% CO2.

extract_protocol:
RNA was harvested using Trizol Reagent (Invitrogen, USA). A total amount of 1 μg RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were were generated using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology (Shanghai) Co., Ltd.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: Peripheral blood

value: HBO1 knockdown


title: m139, H3K27ac, biol rep 1


title: pol32D H3K4me3_eSPAN 25C 30' MNase rep2 [Alb237_pol32D_H3K4me3_eSPAN_S30]


title: pol32D BrdU 25C 30' MNase rep4 [Alb788_pol32D_BrdU_S30]

source_name: pol32D BrdU 25C 30' MNase

value: BrdU


title: HDL111_Lung_TCRAD

source_name: Lung

value: Lung

value: gd T cells

value: pediatric


title: pol32D BrdU 25C 30' MNase rep3 [Alb780_pol32D_BrdU_S30]

value: 25C 30' MNase


title: HDL111_LLN_TCRG

source_name: LLN


title: m18, H3K27ac, biol rep 3


title: NALM-6 cells, shHBO1, rep2


title: m139, IgG,  biol rep 1

value: Esophageal squamous cell carcinoma cells with wild-type p53

value: IgG antibody (Epicypher, #13-0042)

value: wild-type p53


title: HDL111_Jejunum_TCRG

value: Jejunum


title: pol32D Brdu 25C 30' MNase rep2 [Alb236_pol32D_Brdu_S30]

source_name: pol32D Brdu 25C 30' MNase

value: Brdu


title: pol32D Brdu 25C 30' MNase rep1 [Alb114_pol32_Brdu_S30]


title: NALM-6 cells, shHBO1, rep1


title: NALM-6 cells, shControl, rep2

value: WT


title: NALM-6 cells, shControl, rep3


title: HDL111_LLN_TCRAD

value: LLN


title: m18, H3K27ac, biol rep 1

value: Esophageal squamous cell carcinoma cells with p53-R172H mutation

value: H3K27ac antibody (CST, #8173)


title: pol32FFAA H3K56ac_eSPAN 25C 30' MNase rep2 [Alb392_pol32FFAA_H3K56ac_eSPAN_S30]

source_name: pol32FFAA H3K56ac_eSPAN 25C 30' MNase


title: m18_IgG_3, biol rep 3


title: HDL111_Blood_TCRG

source_name: Blood

value: Blood


title: m18, H3K27ac, biol rep 2


title: pol32FFAA H3K56ac_eSPAN 25C 30' MNase rep1 [Alb246_pol32FFAA_H3K56ac_eSPAN_S30]


title: DMD-VSMCs with oxidative stress, bio rep3

city: Tampa

first: Wanling

last: xuan

state: FL

address: 12901 Bruce B Down Blvd

department: DPS

institute: University of South Florida

data_processing:
RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5.
Isoform expression of known Ensembl transcripts were estimated with Salmon version 0.8.2.
Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.
The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.6.2.
Assembly: Genome Reference Consortium Human Build 38
Supplementary files format and content: tab-delimited text files  include CPM values for each Sample

source_name: DMD iPS cell line SC604A

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
Library preparation was performed with 500ng to 1ug of total RNA. Ribosomal RNA was removed by an RNase-H method using RiboErase kits (Kapa Biosystems). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags.

value: DMD iPS cell line SC604A

value: iPS derived vascular smooth muscle cells

value: DMD


title: pol32FFAA H3K4me3_eSPAN 25C 30' MNase rep2 [Alb391_pol32FFAA_H3K4me3_eSPAN_S30]

source_name: pol32FFAA H3K4me3_eSPAN 25C 30' MNase


title: HDL111_Blood_TCRAD


title: m18, IgG, biol rep 2


title: HDL110_Spleen_TCRG

value: Spleen


title: m139, IgG, biol rep 2


title: pol32FFAA H3K4me3_eSPAN 25C 30' MNase rep1 [Alb245_pol32FFAA_H3K4me3_eSPAN_S30]


title: m18, IgG, biol rep 1


title: DMD-VSMCs with oxidative stress, bio rep2


title: DMD-VSMCs with oxidative stress, bio rep1


title: Mouse, intragastric gavage with Lycium chinense Mill, blood

city: Nanjing

first: Xiaozhu

last: Tang

address: Xianlin Road

institute: Nanjing University of Chinese University

description: mice's blood

data_processing:
150 bp paired-end reads were mapped to the reference Lycium chinense Mill by using Bowtie2.  Genome build used for read alignment for Lycium_chinense_Mill.bam and mice_blood.bam was Lycium barbarum chloroplast, complete genome NCBI Reference Sequence: NC_041110.1.  https://www.ncbi.nlm.nih.gov/nuccore/NC_041110.1
Only unique mapping paired reads were sorted using SAMtools and kept for subsequent analysis.
Fastp 0.19.11 software performs basic quality statistics for raw reads. QC analysis was used by fastqc v0.11.5. Burrows Wheeler aligner(0.7.12-r1039) can compare reads to reference genome. Peak calling was performed by MACS22.1.0. The motifs were recognized by Homer findMotifsGenome.pl(v4.9.1).
The file type of mice_blood_peaks_table.tsv was peak file.
Assembly: NC_041110.1
Supplementary files format and content: Peaks file mice_blood_peaks_table.tsv

source_name: blood

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: we intragastric gavaged C57 BL/6J mice with Lycium chinense Mill at a dose of 10 mL/kg. After 14 days, the blood was drawn and subjected to Illumina deep-sequencing technology

value: C57 BL/6J

value: intragastric gavage of mice with Lycium chinense Mill

value: blood


title: pol32FFAA BrdU 25C 30' MNase rep2 [Alb390_pol32FFAA_BrdU_S30]

source_name: pol32FFAA BrdU 25C 30' MNase

value: 25C 30' MNase

value: BrdU


title: pol32FFAA Brdu 25C 30' MNase rep1 [Alb244_pol32FFAA_Brdu_S30]

source_name: pol32FFAA Brdu 25C 30' MNase


title: HDL110_Spleen_TCRAD

value: gd T cells

value: pediatric


title: HDL110_Lung_TCRG

value: Lung


title: HDL111_Jejunum_TCRAD

value: Jejunum


title: WT-VSMCs with oxidative stress, bio rep2

source_name: iPSC cell lines DYS0100

value: iPSC cell lines DYS0100

value: WT


title: NALM-6 cells, shControl, rep1

value: Peripheral blood


title: pol3pip PCNA_eSPAN 25C 30' sonication rep1 [Alb802_pol3pip_PCNA_eSPAN_S30]

source_name: pol3pip PCNA_eSPAN 25C 30' sonication

value: 25C 30' sonication


title: Colon tissue, MG_3, rep2

city: Luzhou

first: Lai

last: Jia

address: Xianglin Road

institute: Southwest Medical University

data_processing:
RNA quality was determined by 2100 Bioanalyser (Agilent, USA) and quantified using the Nanodrop2000
After being quantified by TBS380, the paired-end RNA-seq sequencing library was sequenced with the Illumina HiSeq xten/NovaSeq 6000 sequencer (2×150 bp read length)
functional enrichment analyses, including Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), were performed to identify which DEGs were significantly enriched in GO terms and metabolic pathways at Bonferroni-corrected P values ≤ 0.05 compared with the whole-transcriptome background

source_name: WT C57BL/6J with DSS water

growth_protocol: Acute colitis was induced in mice via administration of 2.5% (w/v) DSS in drinking water. Mice received either regular drinking water (normal group) or 2.5% DSS drinking water (model group and treatment groups) for 8 days followed by regular drinking water for 6 days.

extract_protocol:
TRIzol reagent (Invitrogen, Carlsbad, CA, USA) was used to extract total RNA from colon tissues and RAW264.7 cells on the basis of the instructions of the manufacturer. Single-stranded cDNA was reverse transcribed from RNA by a reverse transcription kit (Vazyme Biotech, China)
The RNA-seq transcriptome library was prepared following the TruSeqTM RNA Sample Preparation Kit from Illumina using 1 μg of total RNA

treatment_protocol: Mice were randomly divided into 6 groups with 10 mice per group: the untreated normal control, model group, low-dose MG group (50 mg/kg), medium-dose MG group (100 mg/kg), high-dose MG group (200 mg/kg) and SASP-positive group (500 mg/kg) that were orally administered once daily for 6 days.

value: Colon

tag: disease state

value: induced acute colitis

value: high-dose of MG  (200 mg/kg)


title: WT-VSMCs with oxidative stress, bio rep1

value: iPS derived vascular smooth muscle cells


title: biol replicate 1-6

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

institute: ETH ZURICH / University of Zurich

data_processing:
SevenBridges Analysis Platform
Raw sequences were provided as input to the BD Rhapsody™ Targeted Analysis Pipeline (Revision 0) using the "Single-Cell Multiplex Kit - Mouse" sample tag selection
The counts for each sample were further analyzed via the standard Seurat pipeline
Assembly: Custom AbSeq panel and amplicon reference
Supplementary files format and content: tab-delimited text file of raw, RSEC, and DBEC-adjusted counts

source_name: B16F10 tumors intradermal

extract_protocol:
Single cell isolation was performed with the BD Rhapsody Express Single-Cell Analysis system according to the manufacturer's protocol (BD Biosciences)
Targeted cDNA library preparation was conducted with the targeted mRNA and AbSeq amplification kit (BD Biosciences), the BD Rhapsody Immune Response Panel and a complementary custom-designed targeted panel. Size distribrution was performed using a D1000 assay on a Tape station system (Agilent).

value: B16F10 tumors intradermal

value: CD4+ T cells

value: Foxp3-Cre(+/-) x Il23rfl/fl

tag: Sex

value: female

tag: timepoint

value: Day 13 after tumor inoculation

value: no treatment


title: HDL110_Jejunum_TCRAD

source_name: Jejunum

value: gd T cells

value: pediatric


title: Colon tissue, MG_2, rep2

tag: genotype


title: HDL093_Spleen_TCRG

source_name: Spleen

value: Spleen


title: pol3pip BrdU 25C 30' sonication rep1 [Alb801_pol3pip_BrdU_S30]

source_name: pol3pip BrdU 25C 30' sonication

tag: batch

value: BrdU


title: DMD-VSMCs, bio rep3

tag: cell line

value: DMD iPS cell line SC604A

value: DMD


title: HDL093_Spleen_TCRAD


title: pol3pip PCNA_ChIP 25C 30' sonication rep1 [Alb800_pol3pip_PCNA_ChIP_S30]

source_name: pol3pip PCNA_ChIP 25C 30' sonication

tag: strain

tag: condition

value: 25C 30' sonication


title: Colon tissue, MG_1, rep2

tag: tissue

value: Colon

value: WT

tag: treatment


title: DMD-VSMCs, bio rep2


title: HDL093_Lung_TCRG

source_name: Lung

value: Lung


title: pol3pip H3K56ac_eSPAN 25C 30' MNase rep2 [Alb766_pol3pip_H3K56ac_eSPAN_S30]

source_name: pol3pip H3K56ac_eSPAN 25C 30' MNase

value: 25C 30' MNase


title: DMD-VSMCs, bio rep1

value: iPS derived vascular smooth muscle cells


title: HDL093_Lung_TCRAD


title: Colon tissue, model_2, rep2

value: induced acute colitis

value: normal saline


title: pol3pip H3K56ac_eSPAN 25C 30' MNase rep1 [Alb702_pol3_pip_H3K56ac_eSPAN_S]


title: WT-VSMCs with oxidative stress, bio rep3

value: iPSC cell lines DYS0100


title: WT-VSMCs, bio rep3


title: HDL093_LLN_TCRG

source_name: LLN

value: LLN


title: WT-VSMCs, bio rep2


title: Colon tissue, normal_3, rep2

source_name: WT C57BL/6J with normal water

value: healthy


title: Colon tissue, model_1, rep2


title: pol3pip H3K4me3_eSPAN 25C 30' MNase rep1 [Alb701_pol3_pip_H3K4me3_eSPAN_S]

source_name: pol3pip H3K4me3_eSPAN 25C 30' MNase


title: HDL093_LLN_TCRAD

value: gd T cells


title: HDL093_Jejunum_TCRAD

value: Jejunum

value: pediatric


title: WT-VSMCs, bio rep1


title: Colon tissue, normal_1, rep2


title: HDL078_Lung_TCRG


title: pol3pip BrdU 25C 30' MNase rep1 [Alb700_pol3_pip_BrdU_S]

source_name: pol3pip BrdU 25C 30' MNase

value: BrdU


title: Colon tissue, normal_2, rep2


title: HAP1 sgRNA3 + HDR temp passage 2 Rep 4 Tn5

city: Ann Arbor

first: Anthony

last: Antonellis

state: MI

address: 1241 Catherine St

department: Human Genetics

institute: University of Michigan

description: Tn5 KARS1 SGE sgRNA3 p2 Rep4

data_processing:
Paired-end reads were trimmed using Cutadapt 4.1
Trimmed reads were mapped to H. sapiens GRCh38 using Bowtie2 2.2.5
Reads mapping to KARS1 Exon 2 in BAM files were assessed for WT genomic DNA sequence, insertions/deletions, and HDR knock-in using custom Python scripts with Pysam 0.21.0
Called reads were converted to BED file using Bedtools 2.31.0
Assembly: H. sapiens GRCh38 (Bowtie2 GRCh38 no-alt analysis set premade index)
Supplementary files format and content: BAM files containing reads mapped to KARS1 Exon 2 (read category indicated in 'CO' tag)
Supplementary files format and content: .txt files containing counts of reads mapped to KARS Exon 2 by read category
Library strategy: Tn5-Seq

growth_protocol: Cells were cultured in IMDM + 10% FBS + 1% pen/strep solution under standard growth conditions in 10 cm cell culture dishes. Cells were passaged by trypsinization every 2-3 days.

extract_protocol:
Total genomic DNA was isolated using the Macherey-Nagel NucleoSpin Tissue Mini DNA extraction kit.
Tn5 transposase conjugated with Illumina/Nextera-compatible adapters was used to simultaneously fragment and ligate adapters onto genomic DNA. Resultant fragments were amplified with Illumina i5/i7 universal primers and unique dual index primers in a subsequent barcode PCR reaction.
Tn5 transposase library preparation with Illumina/Nextera-compatible adapter overhangs and dual indices

treatment_protocol: Cells were transfected via Lipofection with all-in-one pSpCas9+sgRNA+puro constructs with or without KARS1 Exon 2 variant HDR template library containing all possible variants at in-frame codons. Transfected cells were selected with 2.5 ug/mL puromycin for 48 hrs and allowed to recover to 70% confluency. Cells were passaged every 2-3 days for 2 additional passages (p1 and p2).

value: near-haploid cells derived from KBM-7


title: Colon tissue, model_3, rep2


title: HAP1 sgRNA3 + HDR temp passage 2 Rep 3 Tn5

description: Tn5 KARS1 SGE sgRNA3 p2 Rep3


title: Pclaf KO lung epithelial cell, bleomycin 1 week

city: Houston

first: Bongjun

last: Kim

state: Texas

address: 6565 MD Anderson BLVD

department: Experimental Radiation Oncology

institute: MD Anderson Cancer Center

description: 10x genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 by Novogene.
Reads were aligned to GRCm38 reference assembly using STAR aligner7 (v2.7.10a).
Assembly: mm10
Supplementary files format and content: Cell Ranger output (Matrix, Barcodes, and genes)

extract_protocol:
Lung cells were freshly isolated from the digested lung in Leibovitz media with 2 mg/ml collagenase type I, 2 mg/ml elastase , and 0.4 mg/ml DNase I for 45 min at 37 ℃. Then digested lung cells were were resuspended in 400 μl buffer with 5 μl of anti-CD31-FITC, 5 μl of anti-Cd45-APC, and 5 μl anti-CD326 (EpCAM)-PE-Cy7 and incubated for 30 min at 4 °C. After then cells were washed twice followed by sorting of the epithelial cells by FACS
or generating single-cell gene expression libraries, 1.6 X 104 cells per group of single cells were subjected to Chromium Single Cell Gene Expression 3v3.1 kit (10X genomics) at the Single Cell Genomics Core at Baylor College of Medicine. In brief, reverse transcription (RT) reagents, Gel Beads containing barcoded oligonucleotides, and oil were loaded on a Chromium controller (×10 Genomics) to generate single-cell Gel Beads-In-Emulsions (GEMs) where full-length cDNA was synthesized and barcoded for each single cell. Subsequently the GEMs are broken and cDNA from every single cell is pooled. Following cleanup using Dynabeads MyOne Silane Beads, cDNA is amplified by PCR. The amplified product is fragmented to optimal size before end-repair, A-tailing, and adaptor ligation. The final library was generated by amplification.

value: 8 to 10 weeks

value: Epithelial cell

value: Pclaf KO

value: Bleomycin 1 week


title: HDL078_Lung_TCRAD

value: Lung


title: HDL078_Jejunum_TCRG


title: Pclaf WT lung epithelial cell, bleomycin 1 week

description: 10x genomics

value: Pclaf WT

value: Belomycin 1 week


title: HAP1 sgRNA3 + HDR temp passage 2 Rep 2 Tn5

description: Tn5 KARS1 SGE sgRNA3 p2 Rep2


title: rad27 H3K4me3_eSPAN 20 async MNase rep2 [Alb941_rad27_H3K4me3_eSPAN_20async]

source_name: rad27 H3K4me3_eSPAN 20 async MNase

value: 20 async MNase


title: HAP1 sgRNA3 + HDR temp passage 2 Rep 1 Tn5

description: Tn5 KARS1 SGE sgRNA3 p2 Rep1


title: sample.16_Old ANKO5

city: Izumo

first: Jun

last: Yoshino

state: Shimane

address: 89-1 Enya-cho

country: Japan

institute: Faculty of Medicine, Shimane University

description: 16.AGCCATTGCG-ATCCTGCCAG.H7M5YDSXY_AGCCATTGCG-ATCCTGCCAG_S17_L003

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with custom demultiplexer written in python
Technical replicate fastq files were combined and aligned with STAR 2.0.4b
Gene counts dervied with Subread:featureCount 1.45 and annotated with Ensembl Biomart.
Genome_build: Ensembl GRCm38.76
Supplementary_files_format_and_content: Gene counts in tab-delimitted text MS Excel format

source_name: Old ANKO_subcutaneous WAT

growth_protocol: ANKO mice were generated by using adiponectin-Cre transgenic mice and Nampt flox mice.

extract_protocol:
Subcutaneous white adipose tissue samples were removed, flash frozen by liquid nitrogen, and RNA was harvested using Qiazol Reagent with Rneasy Mini Kit (Qiagen).
Ribo-Zero Gold kit

treatment_protocol: Mice were kept at room temperature under a normal regular-chow fed condition.

tag: strain background

tag: genotype/variation

value: ANKO (adipocyte specific Nampt knockout)

value: old (22-27 month-old)

value: Subcutaneous white adipose tissue


title: rad27 H3K56ac_eSPAN 20 async MNase rep1 [Alb633_rad27_H3K56ac_eSPAN_async20]

source_name: rad27 H3K56ac_eSPAN 20 async MNase


title: HAP1 sgRNA3 + HDR temp passage 1 Rep 4 Tn5

description: Tn5 KARS1 SGE sgRNA3 p1 Rep4

tag: cell type


title: rad27 H3K4me3_eSPAN 20 async MNase rep1 [Alb632_rad27_H3K4me3_eSPAN_async20]


title: HDL072_Spleen_TCRG

value: Spleen

tag: developmental stage


title: HAP1 sgRNA3 + HDR temp passage 1 Rep 3 Tn5

description: Tn5 KARS1 SGE sgRNA3 p1 Rep3


title: pol3pip BrdU 25C 30' MNase rep2 [Alb764_pol3pip_BrdU_S30]

value: 25C 30' MNase


title: rad27 BrdU 20 async MNase rep2 [Alb940_rad27_BrdU_20async]

source_name: rad27 BrdU 20 async MNase


title: rad27 H3K56ac_eSPAN 20 async MNase rep2 [Alb942_rad27_H3K56ac_eSPAN_20async]


title: sample.14_Old ANKO3

description: 14.AGACAGACGT-TATCAGTGCA.H7M5YDSXY_AGACAGACGT-TATCAGTGCA_S14_L003

tag: age


title: HDL072_Spleen_TCRAD

value: gd T cells


title: rad27 BrdU 20 async MNase rep1 [Alb631_rad27_BrdU_async20]


title: sample.13_Old ANKO2

description: 13.CACCATTGTA-TACCAATTGC.H7M5YDSXY_CACCATTGTA-TACCAATTGC_S23_L003


title: HAP1 sgRNA3 + HDR temp passage 1 Rep 1 Tn5

description: Tn5 KARS1 SGE sgRNA3 p1 Rep1


title: HDL072_MLN_TCRG

source_name: MLN

value: MLN

value: pediatric


title: HDL072_MLN_TCRAD


title: HAP1 sgRNA3 + HDR temp passage 1 Rep 2 Tn5

description: Tn5 KARS1 SGE sgRNA3 p1 Rep2

value: near-haploid cells derived from KBM-7


title: sample.12_Old ANKO1

description: 12.AAGACTCTCG-TAAGTCTGGC.H7M5YDSXY_AAGACTCTCG-TAAGTCTGGC_S4_L003


title: HDL072_Lung_TCRG


title: sample.11_Old flox/flox5

description: 11.CAATTCACGC-ACATCCTGCG.H7M5YDSXY_CAATTCACGC-ACATCCTGCG_S21_L003

source_name: Old flox/flox_subcutaneous WAT

value: flox/flox (control)


title: WT PCNA_eSPAN 30C 45' HU sonication rep2 [Alb518_WT_PCNA_eSPAN_S45]

source_name: WT PCNA_eSPAN 30C 45' HU sonication

value: 30C 45' HU sonication

value: WT


title: WT PCNA_eSPAN 30C 45' HU sonication rep1 [Alb404_WT_PCNA_eSPAN_S45]


title: sample.10_Old flox/flox4

description: 10.CCACCTTCAA-ACCATCGAGG.H7M5YDSXY_CCACCTTCAA-ACCATCGAGG_S31_L003


title: WT PCNA_ChIP 30C 45' HU sonication rep2 [Alb516_WT_PCNA_ChIP_S45]

source_name: WT PCNA_ChIP 30C 45' HU sonication


title: HDL072_Lung_TCRAD


title: HAP1 sgRNA3 + GFP control passage 2 Tn5

description: Tn5 sgRNA3 only control p2


title: HDL078_Jejunum_TCRAD

source_name: Jejunum

value: Jejunum


title: sample.15_Old ANKO4

description: 15.AGAAGGAACA-TGGTAGATGC.H7M5YDSXY_AGAAGGAACA-TGGTAGATGC_S12_L003


title: HAP1 sgRNA1 + HDR temp passage 2 Rep 4 Tn5

description: Tn5 KARS1 SGE sgRNA1 p2 Rep4


title: WT PCNA_ChIP 30C 45' HU sonication rep1 [Alb402_WT_PCNA_ChIP_S45]


title: HDL072_LLN_TCRG

value: LLN


title: WT BrdU 30C 45' HU sonication rep2 [Alb517_WT_BrdU_S45]

source_name: WT BrdU 30C 45' HU sonication

value: BrdU


title: sample.9_Old flox/flox3

description: 9.CGGTGTTCCT-ATGCAACCAG.H7M5YDSXY_CGGTGTTCCT-ATGCAACCAG_S53_L003


title: sample.8_Old flox/flox2

description: 8.CCGACTCAGA-TTAACGAGCA.H7M5YDSXY_CCGACTCAGA-TTAACGAGCA_S36_L003


title: HAP1 sgRNA1 + HDR temp passage 2 Rep 3 Tn5

description: Tn5 KARS1 SGE sgRNA1 p2 Rep3


title: HDL072_LLN_TCRAD


title: WT BrdU 30C 45' HU sonication rep1 [Alb403_WT_BrdU_S45]


title: HDL072_Jejunum_TCRG


title: sample.7_Old flox/flox1

description: 7.CCTCAGCGAA-TGTGGAATAG.H7M5YDSXY_CCTCAGCGAA-TGTGGAATAG_S40_L003


title: sample.6_Young ANKO3

description: 6.CGAACTTGAG-TTATGGTGGT.H7M5YDSXY_CGAACTTGAG-TTATGGTGGT_S47_L003

source_name: Young ANKO_subcutaneous WAT

value: young (2 month-old)


title: HAP1 sgRNA1 + HDR temp passage 2 Rep 2 Tn5

description: Tn5 KARS1 SGE sgRNA1 p2 Rep2


title: HAP1 sgRNA1 + HDR temp passage 2 Rep 1 Tn5

description: Tn5 KARS1 SGE sgRNA1 p2 Rep1


title: HAP1 sgRNA1 + HDR temp passage 1 Rep 4 Tn5

description: Tn5 KARS1 SGE sgRNA1 p1 Rep4


title: WT H3K4me3_eSPAN 30C 45' HU rep1 [ASC007_WT_S_H3K4me3_eSPAN]

source_name: WT H3K4me3_eSPAN 30C 45' HU


title: HAP1 sgRNA3 + GFP control passage 1 Tn5

description: Tn5 sgRNA3 only control p1


title: HDL072_Jejunum_TCRAD


title: HDL072_Blood_TCRG

source_name: Blood

value: Blood


title: sample.5_Young ANKO2

description: 5.TCGCTTGCAC-ATCAGTCCTA.H7M5YDSXY_TCGCTTGCAC-ATCAGTCCTA_S64_L003

value: ANKO (adipocyte specific Nampt knockout)


title: HDL072_Blood_TCRAD


title: WT Brdu 30C 45' HU rep1 [ASC006_WT_S_Brdu]

source_name: WT Brdu 30C 45' HU

value: Brdu


title: WT PCNA_eSPAN 25C 40' sonication rep2 [Alb586_WT_PCNA_eSPAN_S40]

source_name: WT PCNA_eSPAN 25C 40' sonication

value: 25C 40' sonication


title: HAP1 sgRNA1 + HDR temp passage 1 Rep 3 Tn5

description: Tn5 KARS1 SGE sgRNA1 p1 Rep3


title: sample.4_Young ANKO1

description: 4.CATAGTCACA-ACGAGGACCA.H7M5YDSXY_CATAGTCACA-ACGAGGACCA_S28_L003

value: Subcutaneous white adipose tissue


title: HAP1 sgRNA1 + HDR temp passage 1 Rep 2 Tn5

description: Tn5 KARS1 SGE sgRNA1 p1 Rep2


title: HDL052_Lung_TCRG

source_name: Lung

value: Lung


title: sample.3_Young flox/flox3

description: 3.CAGCATGAGC-TTACCGATTC.H7M5YDSXY_CAGCATGAGC-TTACCGATTC_S26_L003

source_name: Young flox/flox_subcutaneous WAT


title: HDL052_Lung_TCRAD

value: gd T cells


title: WT PCNA_eSPAN 25C 40' Sonication rep1 [Alb144_WT_PCNA_eSPAN_S40]

source_name: WT PCNA_eSPAN 25C 40' Sonication

value: 25C 40' Sonication


title: HAP1 sgRNA1 + HDR temp passage 1 Rep 1 Tn5

description: Tn5 KARS1 SGE sgRNA1 p1 Rep1


title: HAP1 sgRNA1 + GFP control passage 2 Tn5

description: Tn5 sgRNA1 only control p2


title: sample.2_Young flox/flox2

description: 2.AGGTCCATTC-TCAATGAGGT.H7M5YDSXY_AGGTCCATTC-TCAATGAGGT_S20_L003


title: WT PCNA_ChIP 25C 40' sonication rep2 [Alb584_WT_PCNA_ChIP_S40]

source_name: WT PCNA_ChIP 25C 40' sonication


title: sample.1_Young flox/flox1

description: 1.AATCATCTGG-GAACCACAGG.H7M5YDSXY_AATCATCTGG-GAACCACAGG_S6_L003


title: WT H3K56ac_eSPAN 30C 45' HU rep1 [ASC008_WT_S_H3K56ac_eSPAN]

source_name: WT H3K56ac_eSPAN 30C 45' HU


title: HDL052_Jejunum_TCRG

value: pediatric


title: HAP1 sgRNA1 + GFP control passage 1 Tn5

description: Tn5 sgRNA1 only control p1

value: near-haploid cells derived from KBM-7


title: WT PCNA_ChIP 25C 40' Sonication rep1 [Alb142_WT_PCNA_ChIP_S40]

source_name: WT PCNA_ChIP 25C 40' Sonication


title: HDL052_Jejunum_TCRAD


title: HDR template library pDNA Tn5

description: Tn5 Input HDR template library Rep 1

library_source: other

molecule: other


title: D509_Spleen_TCRG

source_name: Spleen

value: Spleen

value: adult


title: WT BrdU 25C 40' sonication rep2 [Alb585_WT_BrdU_S40]

source_name: WT BrdU 25C 40' sonication

value: WT


title: SI02A2

city: Zhuhai

first: Yujiao

last: Gong

address: No. 52 Mei Hua Dong Road

institute: The Fifth Affiliated Hospital of Sun Yat-sen University

data_processing:
ZebraCallV2 1.0.8.208
The sequencing data was filtered with SOAPnuke (v1.5.2)
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4)
Ericscript (v0.5.5) [4] and rMATS (V3.2.5)[5] were used to fusion genes and differential splicing genes (DSGs), respectively
Bowtie2 (v2.2.5) was applied to align the clean reads to the gene set, a database for this organism built by BGI (Beijing Genomic Institute in ShenZhen), which known and novel, coding transcripts were included, then expression level of gene was calculated by RSEM (v1.2.12)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: HASMC

growth_protocol: HASMC were maintained in SMCM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted from the cells using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction.
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented   into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was   generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA   synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end   repair. The cDNA fragments obtained from previous step were amplified by PCR, and products   were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on   the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products   from previous step were heated denatured and circularized by the splint oligo sequence to get the   final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The   final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300   copies of one molecular, DNBs were loaded into the patterned nanoarray and pair end 100 bases   reads were generated on BGIseq500 platform (BGI-Shenzhen, China)

treatment_protocol: To delivery siRNA into VSMC, LipofectamineTM 3000 Transfection Reagent (Invitrogen) were used essentially following the manufacturer's protocol. After 48 hours VSMC were harvested to extract total RNA.

value: HASMC

value: vasuclar smooth muscle cells

value: DDX24 knockdown


title: WT Brdu 25C 40' Sonication rep1 [Alb143_WT_Brdu_S40]

data_processing:
Raw reads were firstly trimmed by Cutadapt (Marcel, 2011) to remove adapters and low quality reads, and then mapped to the yeast genome (sacCer3) using Bowtie2 (Langmead and Salzberg, 2012).Duplicate reads were further filtered by Sambamba (Tarasov et al., 2015) to remove PCR duplication.
The genome-wide read coverage on Watson and Crick strands were calculated at the bin of 1bp using deepTools bamCoverage (Ramirez et al., 2016). Then, the raw genome-wide read coverage was normalized with the number of total mapped reads to obtain counts per million value (CPM).
Spike-in added samples normalization. For each Sonication-BrdU-IP-ssSeq sample, the raw genome-wide coverage was normalized using the formula: BrdUsoni = (BrdUcov / BrdUspike) / (Inputread / Inputspike). BrdUcov is the raw coverage of BrdU-IP-ssSeq; BrdUspike is the number of total mapped spike-in reads (S. pombe reads) in BrdU sample, Inputread is the number of total mapped reads in input, and Inputspike is the number of total mapped spike-in reads (S. pombe) in input. In this way, BrdU incorporation at each strain was quantified as BrdUsoni.
Spike in added samples normalization. For each MNase-BrdU-IP-ssSeq dataset, reads with the nucleosome sized (120~170bp) were first selected to calculate the raw coverage of nucleosome occupancy surrounding replication origins, and then normalized using the formula: BrdUMNase = (BrdUcov-MNase / BrdUspike-MNase) / (Inputread-MNase / Inputspike-MNase). BrdUcov-MNase is the raw coverage of the nucleosome-sized reads, BrdUspike-MNase is the number of mapped nucleosome-sized spike-in reads in the same sample, Inputread-MNase is the number of mapped  nucleosome-sized reads in input, and Inputspike-MNase is the number of mapped nucleosome-sized spike-in reads in the same input sample. In this way, the nucleosome occupancy on nascent chromatin was quantified as BrdUMNase.
Assembly: saccer3
Supplementary files format and content: tar of bw, bigwig format, CPM which is normalized by total number of reads
Supplementary files format and content: tar of bw, bigwig format, BrdU coverage normalized by spike-in and input described as formulas above.

source_name: WT Brdu 25C 40' Sonication

extract_protocol:
For analysis of DNA replication by BrdU-IP-ssSeq, and PCNA ChIP and eSPAN experiments, chromatin was fragmented by sonication (15 seconds on and 30 seconds off for 10 cycles in a Bioruptor Pico, Diagenode). For analysis of nucleosome occupancy at nascent chromatin, H3K4me3 and H3K56ac ChIP as well as almost all eSPAN experiments except those marked by sonication, chromatin was digested with MNase to map nucleosomes (Wal and Pugh, 2012).
The ssDNA libraries were prepared using the Accel-NGS 1S Plus kit (Cat no. 10096, Swift Bioscience).


title: D509_Spleen_TCRAD


title: SI02A1


title: D509_MLN_TCRAD

source_name: MLN

value: MLN


title: WT PCNA_eSPAN 25C 30' sonication rep2 [Alb198_WT_PCNA_eSPAN_S30]

source_name: WT PCNA_eSPAN 25C 30' sonication

value: 25C 30' sonication


title: HAP1 sgRNA3 + HDR temp passage 3 Rep 3

description: TileSeq KARS1 SGE sgRNA3 p3 Rep3

data_processing:
fastq read quality was assessed using FastQC v0.12.1
Paired-end reads were merged using BBMerge 37.62
Merged reads were trimmed using Cutadapt 4.1
Reads in fastq files were directly parsed using Biopython 1.81 and tabulated to generate count files for variant calling
Custom Python scripts were used to calculate enrichment scores for variants with at least 10 reads across p0 replicates by calculating log2 ratios of variant frequency at a given passage / average HDR template frequency
Assembly: NA
Supplementary files format and content: .txt files with counts of all unique sequences identified for a given fastq file after merging and trimming (*merge_trim_counts.txt)
Library strategy: Tile-Seq

extract_protocol:
Total genomic DNA was isolated using the Macherey-Nagel NucleoSpin Tissue Mini DNA extraction kit.
Genomic DNA was amplified using PCR primers outside the KARS1 Exon 2 locus (~3 kb product) followed by direct amplification of the exon 2 region of interest using region-specific primers with Illumina-compatible adapter overhangs. Resultant PCR products were amplified with Illumina i5/i7 universal primers and unique dual index primers.
Fixed-amplicon sequencing with KAPA HiFi polymerase and Illumina-compatible adapter overhangs

treatment_protocol: Cells were transfected via Lipofection with all-in-one pSpCas9+sgRNA+puro constructs with or without KARS1 Exon 2 variant HDR template library containing all possible variants at in-frame codons. Transfected cells were selected with 2.5 ug/mL puromycin for 48 hrs and allowed to recover to 70% confluency (p0) before passaging into IMDM media + galactose for the remainder of the experiment.


title: HAP1 sgRNA3 + HDR temp passage 3 Rep 4

description: TileSeq KARS1 SGE sgRNA3 p3 Rep4


title: WT PCNA_eSPAN 25C 30' Sonication rep1 [Alb140_WT_PCNA_eSPAN_S30]

source_name: WT PCNA_eSPAN 25C 30' Sonication

value: 25C 30' Sonication


title: SI01A2


title: D509_Lung_TCRG

data_processing:
Raw data were processed using the standard immunoSEQ Analyzer from Adaptive Biotechnologies Corporation.
Assembly: Third party provider description: "Sequences were not aligned against a reference genome; instead they were aligned and annotated based on our custom pipeline using primers designed to IMGT reference V and J genes. The CDR3 regions were defined as per IMGT beginning with the second conserved cysteine encoded by 3’ portion of V gene segment. IMGT reference: Yousfi Monod, M., Giudicelli, V., Chaume, D. & Lefranc, M. P. IMGT/JunctionAnalysis: the first tool for the analysis of the immunoglobulin and T cell receptor complex V-J and V-D-J JUNCTIONs. Bioinformatics 20, (Suppl 1): i379–i385 (2004).
Supplementary files format and content: Processed data files are in the form of tsv files containing clonal counts, nt and aa sequences, as well as VDJ subtype information

extract_protocol:
DNA was isolated from cell pellets using the DNA micro kit (Qiagen) and DNA concentrations were assessed using the NanoDrop (Thermo Scientific).
Other


title: HAP1 sgRNA3 + HDR temp passage 3 Rep 1

description: TileSeq KARS1 SGE sgRNA3 p3 Rep1


title: WT PCNA_ChIP 25C 30' sonication rep2 [Alb196_WT_PCNA_ChIP_S30]

source_name: WT PCNA_ChIP 25C 30' sonication


title: SI01A1


title: D509_Lung_TCRAD


title: WT PCNA_ChIP 25C 30' Sonication rep1 [Alb138_WT_PCNA_ChIP_S30]

source_name: WT PCNA_ChIP 25C 30' Sonication


title: D509_LLN_TCRG

source_name: LLN

value: LLN


title: SI02A3


title: NC3

value: negative control


title: NC2


title: HAP1 sgRNA3 + HDR temp passage 2 Rep 3

description: TileSeq KARS1 SGE sgRNA3 p2 Rep3


title: HAP1 sgRNA3 + HDR temp passage 2 Rep 4

description: TileSeq KARS1 SGE sgRNA3 p2 Rep4


title: NC1


title: D509_Jejunum_TCRAD

source_name: Jejunum

value: Jejunum


title: SI01A3


title: HAP1 sgRNA3 + HDR temp passage 2 Rep 2

description: TileSeq KARS1 SGE sgRNA3 p2 Rep2


title: WT H3K56ac_eSPAN 25C 30' sonication rep1 [Alb178_WT_H3K56ac_eSPAN_S30]

source_name: WT H3K56ac_eSPAN 25C 30' sonication


title: HAP1 sgRNA3 + HDR temp passage 3 Rep 2

description: TileSeq KARS1 SGE sgRNA3 p3 Rep2


title: HAP1 sgRNA3 + HDR temp passage 2 Rep 1

description: TileSeq KARS1 SGE sgRNA3 p2 Rep1


title: D505_Spleen_TCRG


title: WT H3K4me3_eSPAN 25C 30' sonication rep1 [Alb177_WT_H3K4me3_eSPAN_S30]

source_name: WT H3K4me3_eSPAN 25C 30' sonication


title: HAP1 sgRNA3 + HDR temp passage 1 Rep 4

description: TileSeq KARS1 SGE sgRNA3 p1 Rep4


title: WT H3K4me3_eSPAN 25C 30' sonication rep2 [Alb357_WT_H3K4me3_eSPAN_S30]


title: D505_Spleen_TCRAD


title: D505_Lung_TCRAD

source_name: Lung

value: Lung


title: IL-36Rafl/fl-1

first: Dalin

last: Chen

address: 295 Changxing Road

institute: Guangdong Institute of Orthopedics

data_processing:
The raw data obtained from sequencing was filtered using SOAPnuke (v1.5.6) to obtain clean data. Follow-up use of Dr. Tom's Multi-Omics Data Mining System (https://biosys.bgi.com) is used for data analysis, mapping and mining.
HISTA2 (v2.1.0)[2] software was used to align the clean data to the reference genome. Then, Ericscript (v0.5.5) was used for gene fusion detection and rMATS (v3.2.5) was used for alternative splicing and differential alternative splicing detection.
Align the clean data to the reference gene set using Bowtie2 (v2.3.4.3). Gene expression quantification was performed using RSEM (v1.3.1) software, and clustering heat maps of gene expression in different samples were plotted using pheatmap (v1.0.8).
Differential gene detection was performed using DESeq2 (v1.4.5) under conditions of Q value≤0.05 or FDR≤0.001.
GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of differential genes were performed using Phyper, and Qvalue≤0.05 was used as the threshold, which was defined as significant enrichment in candidate genes.
Assembly: GCF_000001635.27_GRCm39
Supplementary files format and content: This project uses SOAPnuke, a filtering software independently developed by Shenzhen BGI, for filtering. The filtered "Clean Reads" are saved in FASTQ format.

source_name: mouse epidermis keratinocyte

extract_protocol:
Lyse the tissue using Trizol, centrifuge and transfer the supernatant into an EP tube containing chloroform/isoamyl alcohol (24:1) and mix well. After centrifugation, transfer the supernatant into a new EP tube containing isopropyl alcohol and mix well, then let it stand for 2 hours at (-20°C). After washing, wash 3 times with 75% ethanol. Finally, discard the supernatant and absorb the remaining liquid. After drying, add 20-200 μL DEPC water to dissolve the precipitate.
After quality inspection of the RNA, the secondary structure is opened through denaturation, and oligo(dT) magnetic beads are used to enrich the mRNA. Then a fragmentation reagent is added to fragment the mRNA, a reaction system is prepared, and the reaction program is set to synthesize one-strand and two-strand cDNA. Repair the double-stranded cDNA end, add an A base to the 3' end, and connect the adapter to the cDNA. PCR amplification is then performed, and uncirculated linear DNA molecules are digested. The single-stranded circular DNA molecule is then replicated through rolling circles to form a DNA nanoball (DNB) containing multiple copies. The obtained DNBs are added to the mesh holes on the chip using high-density DNA nanochip technology, and sequenced through combined probe anchored polymerization technology (cPAS).

value: mouse epidermis keratinocyte


title: IL-36Rafl/fl-2


title: HAP1 sgRNA3 + HDR temp passage 1 Rep 2

description: TileSeq KARS1 SGE sgRNA3 p1 Rep2


title: WT H3K56ac_eSPAN 25C 30' sonication rep2 [Alb358_WT_H3K56ac_eSPAN_S30]

first: zhiguo

last: zhang


title: WT Brdu 25C 30' sonication rep3 [Alb197_WT_Brdu_S30]

source_name: WT Brdu 25C 30' sonication

value: Brdu


title: D509_LLN_TCRAD

value: gd T cells


title: D505_LLN_TCRG


title: IL-36Ra-cKO-1

value: IL-36Ra knockdown


title: HAP1 sgRNA3 + HDR temp passage 1 Rep 1

description: TileSeq KARS1 SGE sgRNA3 p1 Rep1

value: near-haploid cells derived from KBM-7


title: D505_Jejunum_TCRAD

value: adult


title: WT Brdu 25C 30' sonication rep2 [Alb176_WT_Brdu_S30]

value: WT


title: WT Brdu 25C 30' Sonication rep1 [Alb139_WT_Brdu_S30]

source_name: WT Brdu 25C 30' Sonication


title: HAP1 sgRNA3 + HDR temp passage 0 Rep 4

description: TileSeq KARS1 SGE sgRNA3 p0 Rep4


title: D484_Spleen_TCRG

source_name: Spleen

value: Spleen


title: WT H3K56ac_eSPAN 25C 30' MNase rep2 [Alb571_WT_H3K56ac_eSPAN_S30]

source_name: WT H3K56ac_eSPAN 25C 30' MNase

value: 25C 30' MNase


title: D484_Spleen_TCRAD


title: WT H3K56ac_eSPAN 25C 30' MNase rep1 [Alb477_WT_H3K56ac_eSPAN_S30]


title: HAP1 sgRNA3 + HDR temp passage 0 Rep 2

description: TileSeq KARS1 SGE sgRNA3 p0 Rep2


title: D505_LLN_TCRAD


title: WT H3K4me3_eSPAN 25C 30' MNase rep2 [Alb570_WT_H3K4me3_eSPAN_S30]

source_name: WT H3K4me3_eSPAN 25C 30' MNase


title: WT BrdU 25C 30' sonication rep4 [Alb356_WT_BrdU_S30]

source_name: WT BrdU 25C 30' sonication

value: BrdU


title: HAP1 sgRNA3 + HDR temp passage 1 Rep 3

description: TileSeq KARS1 SGE sgRNA3 p1 Rep3


title: IL-36Ra-cKO-2


title: D484_Lung_TCRG


title: D484_Lung_TCRAD


title: HAP1 sgRNA3 + GFP control

description: TileSeq sgRNA3 only control


title: HAP1 sgRNA3 + HDR temp passage 0 Rep 3

description: TileSeq KARS1 SGE sgRNA3 p0 Rep3


title: Colon tissue, model_3, rep2

data_processing:
DNA concentrations were quantified by a Nanodrop spectrophotometer (Thermo Scientific Inc., Waltham, MA, USA), and the purity was tested on 1% agarose gel
Qualified samples were subsequently amplified the hypervariable region V3-V4 of the bacterial 16S rRNA gene with the primer pairs 338F (5’-ACTCCTACGGGAGGCAGCA-3’) and 806R (5’-GGACTACHVGGGTWTCTAAT-3’) by an ABI GeneAmp® 9700 PCR thermocycler
Following that, the samples were sequenced on an Illumina MiSeq PE300 platform
Operational taxonomic units (OTUs) clustering was identified at 97% sequence identity
The similarity among the microbial communities in different samples was determined by principal coordinate analysis (PCoA) based on Bray‒Curtis
The PERMANOVA test was used to assess the percentage of variation explained by the treatment along with its statistical significance using Vegan v2.5-3 package
The linear discriminant analysis (LDA) effect size (LEfSe) was performed to identify the significantly abundant taxa (phylum to genera) of bacteria among the different groups
Library strategy: 16S rRNA seq

organism: mouse gut metagenome

source_name: WT C57BL/6J with DSS water

extract_protocol:
the E.Z.N.A.® Soil DNA Kit (Omega Bio-Tek, Norcross, GA, USA) was used to extract the total genomic DNA from the colon.
The RNA-seq transcriptome library was prepared following the TruSeqTM RNA Sample Preparation Kit from Illumina using 1 μg of total RNA

value: Colon

value: induced acute colitis

value: normal saline


title: HAP1 sgRNA1 + HDR temp passage 3 Rep 4

description: TileSeq KARS1 SGE sgRNA1 p3 Rep4


title: WT H3K4me3_eSPAN 25C 30' MNase rep1 [Alb476_WT_H3K4me3_eSPAN_S30]


title: WT BrdU 25C 30' MNase rep2 [Alb569_WT_BrdU_S30]

source_name: WT BrdU 25C 30' MNase


title: Colon tissue, model_2, rep2


title: HAP1 sgRNA1 + HDR temp passage 3 Rep 3

description: TileSeq KARS1 SGE sgRNA1 p3 Rep3


title: D484_LLN_TCRG

value: LLN


title: WT BrdU 25C 30' MNase rep1 [Alb475_WT_BrdU_S30]


title: Colon tissue, model_1, rep2


title: D484_LLN_TCRAD


title: Colon tissue, model_4, rep2


title: Colon tissue, MG_7, rep2

value: MG


title: HAP1 sgRNA3 + HDR temp passage 0 Rep 1

description: TileSeq KARS1 SGE sgRNA3 p0 Rep1


title: HAP1 sgRNA1 + HDR temp passage 3 Rep 2

description: TileSeq KARS1 SGE sgRNA1 p3 Rep2


title: mcm23A input 25C 30' sonication add S.pombe spike in rep4 [Alb1037_mcm23A_input_S30]

description: add S.pombe spike in

value: 25C 30' sonication

value: input


title: D484_Jejunum_TCRG

value: Jejunum


title: HAP1 sgRNA1 + HDR temp passage 3 Rep 1

description: TileSeq KARS1 SGE sgRNA1 p3 Rep1


title: D484_Jejunum_TCRAD


title: mcm23A input 25C 30' sonication add S.pombe spike in rep3 [Alb1013_mcm23A_input_S30]

description: add S.pombe spike in


title: mcm23A Input 25C 30' sonication add S.pombe spike in rep2 [Alb887_mcm23A_Input_S30]

description: add S.pombe spike in

value: Input


title: D300_Jejunum_TCRG

value: gd T cells


title: Colon tissue, MG_5, rep2


title: Colon tissue, MG_6, rep2


title: HAP1 sgRNA1 + HDR temp passage 2 Rep 4

description: TileSeq KARS1 SGE sgRNA1 p2 Rep4


title: HAP1 sgRNA1 + HDR temp passage 2 Rep 3

description: TileSeq KARS1 SGE sgRNA1 p2 Rep3


title: D300_Jejunum_TCRAD


title: D229_MLN_TCRG

source_name: MLN

value: MLN


title: Colon tissue, MG_4, rep2


title: mcm23A BrdU 25C 30' sonication add S.pombe spike in rep4 [Alb1045_mcm23A_BrdU_S30]

description: add S.pombe spike in


title: Colon tissue, MG_3, rep2


title: HAP1 sgRNA1 + HDR temp passage 2 Rep 1

description: TileSeq KARS1 SGE sgRNA1 p2 Rep1

value: near-haploid cells derived from KBM-7


title: mcm23A BrdU 25C 30' sonication add S.pombe spike in rep3 [Alb1025_mcm23A_BrdU_S30]

description: add S.pombe spike in


title: Colon tissue, MG_2, rep2

source_name: WT C57BL/6J with normal water


title: D229_MLN_TCRAD

value: adult


title: mcm23A Input 25C 30' sonication add S.pombe spike in rep1 [Alb825_mcm23A_Input_S30]

description: add S.pombe spike in


title: D229_Lung_TCRG

value: Lung


title: mcm23A BrdU 25C 30' sonication add S.pombe spike in rep2 [Alb899_mcm23A_BrdU_S30]

description: add S.pombe spike in


title: Colon tissue, MG_1, rep2


title: HAP1 sgRNA1 + HDR temp passage 1 Rep 3

description: TileSeq KARS1 SGE sgRNA1 p1 Rep3


title: mcm23A BrdU 25C 30' sonication add S.pombe spike in rep1 [Alb837_mcm23A_BrdU_S30]

description: add S.pombe spike in


title: Colon tissue, normal_6, rep2

value: healthy


title: D229_LLN_TCRG


title: HAP1 sgRNA1 + HDR temp passage 1 Rep 2

description: TileSeq KARS1 SGE sgRNA1 p1 Rep2


title: mcm23A input 25C 30' MNase add S.pombe spike in rep4 [Alb1038_mcm23A_input_S30]

description: add S.pombe spike in

value: 25C 30' MNase


title: D229_LLN_TCRAD


title: mcm23A input 25C 30' MNase add S.pombe spike in rep3 [Alb1014_mcm23A_input_S30]

description: add S.pombe spike in


title: HAP1 sgRNA1 + HDR temp passage 1 Rep 1

description: TileSeq KARS1 SGE sgRNA1 p1 Rep1


title: Colon tissue, normal_4, rep2


title: HAP1 sgRNA1 + HDR temp passage 2 Rep 2

description: TileSeq KARS1 SGE sgRNA1 p2 Rep2


title: HAP1 sgRNA1 + HDR temp passage 0 Rep 4

description: TileSeq KARS1 SGE sgRNA1 p0 Rep4


title: mcm23A Input 25C 30' MNase add S.pombe spike in rep2 [Alb888_mcm23A_Input_S30]

description: add S.pombe spike in


title: D209_Spleen_TCRAD

value: Spleen


title: Colon tissue, normal_3, rep2

value: Colon


title: HAP1 sgRNA1 + HDR temp passage 0 Rep 3

description: TileSeq KARS1 SGE sgRNA1 p0 Rep3


title: Colon tissue, normal_2, rep2


title: mcm23A Input 25C 30' MNase add S.pombe spike in rep1 [Alb826_mcm23A_Input_S30]

description: add S.pombe spike in


title: mcm23A BrdU 25C 30' MNase add S.pombe spike in rep4 [Alb1046_mcm23A_BrdU_S30]

description: add S.pombe spike in

value: BrdU


title: Colon tissue, normal_1, rep2


title: HAP1 sgRNA1 + HDR temp passage 1 Rep 4

description: TileSeq KARS1 SGE sgRNA1 p1 Rep4


title: HAP1 sgRNA1 + HDR temp passage 0 Rep 2

description: TileSeq KARS1 SGE sgRNA1 p0 Rep2


title: D209_MLN_TCRAD


title: mcm23A BrdU 25C 30' MNase add S.pombe spike in rep3 [Alb1026_mcm23A_BrdU_S30]

description: add S.pombe spike in


title: HAP1 sgRNA1 + HDR temp passage 0 Rep 1

description: TileSeq KARS1 SGE sgRNA1 p0 Rep1


title: Colon tissue, normal_5, rep2


title: mcm23A BrdU 25C 30' MNase add S.pombe spike in rep2 [Alb900_mcm23A_BrdU_S30]

description: add S.pombe spike in


title: RB_52

type: genomic

city: Essen

first: Petra

last: Ketteler

address: Hufelandstraße 55

institute: University Hospital Essen

description:
primary retinoblastoma tumor
ryl_et_al_beta_matrix_tumors.txt

hyb_protocol: Bisulfite treatment, whole-genome DNA amplification, hybridization and single-base extension, fluorescence staining and scanning of the chips were performed following the manufacturer´s instructions (Illumina).

scan_protocol: Standard Illumina Protocol

data_processing:
IDAT files generated on 450k and EPIC arrays were reduced to the 450K common probes and processed using minfi (version 1.36).  minfi's funnorm function was used for normalisation.  Batch correction was conducted for each array type using comBat (from sva version 3.42).
matrix processed value definition:  Normalized (minfi funnorm) Average Beta

label: Cy5 and Cy3

source_name: retinoblastoma tumor, primary

label_protocol: Standard Illumina Protocol

extract_protocol: DNA from fresh-frozen tumor samples and retinoblastoma cell lines was isolated as previously described (Lohmann et al., 1997, Schwermer et al., 2019)

value: retinoblastoma

value: C

tag: growth protocol


title: RB_51

value: B


title: D209_Spleen_TCRG

first: Joshua

last: Gray


title: HDR template library pDNA, Rep 2

description: TileSeq Input HDR template library Rep 2


title: mcm23A BrdU 25C 30' MNase add S.pombe spike in rep1 [Alb838_mcm23A_BrdU_S30]

address: 1130 St. Nicholas Avenue

description: add S.pombe spike in


title: D203_Spleen_TCRG


title: RB_49

value: A


title: HDR template library pDNA, Rep 1

description: TileSeq Input HDR template library Rep 1


title: RB_48


title: D209_MLN_TCRG


title: RB_47


title: mcm23Apol32D Input 25C 30' sonication add S.pombe spike in rep1 [Alb831_mcm23Apol32D_Input_S30]

description: add S.pombe spike in

value: 25C 30' sonication


title: mcm23Apol32D Input 25C 30' sonication add S.pombe spike in rep2 [Alb893_mcm23Apol32D_Input_S30]

description: add S.pombe spike in


title: Control3

city: Shanghai

first: Zongfei

last: Ji

address: No. 180, Fenglin Road

institute: Zhongshan hospital, Fudan University

description: 10x Genomics

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Graph-based clustering was performed to cluster cells according to their gene expression profile using the FindClusters function in Seurat. The FindAllMarkers function in Seurat was used to identify marker genes of each cluster. For a given cluster, FindAllMarkers identified positive markers compared with all other cells. Multimodal intersection analysis (MIA) was then used with the reference transcriptomic datasetsnto infer the origin of each of the single cells independently and identify cell types.
We determined the developmental pseudotime and selected ordering genes with the Monocle2 package . Dimensional reduction clustering analysis was performed with the reduceDimension function, followed by trajectory inference with the orderCells function using default parameters.
Cell-cell communication was analyzed using CellPhoneDB
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: retroperitoneum tissue

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: control

value: retroperitoneum tissue

tag: specimen source

value: surgery

value: female


title: D203_MLN_TCRG

address: 630 168th Street

institute: Columbia University

value: MLN

value: gd T cells


title: mcm23Apol32D BrdU 25C 30' sonication add S.pombe spike in rep2 [Alb908_mcm23Apol32D_BrdU_S30]

city: New York

description: add S.pombe spike in


title: Control2

description: 10x Genomics

tag: disease state


title: D203_Spleen_TCRAD

value: adult


title: D203_MLN_TCRAD


title: Control1

description: 10x Genomics

tag: Sex


title: D209_Lung_TCRAD

value: Lung


title: HAP1 sgRNA1 + GFP control

description: TileSeq sgRNA1 only control

value: near-haploid cells derived from KBM-7


title: RB_45


title: D203_LLN_TCRG

source_name: LLN

value: LLN


title: D209_Lung_TCRG


title: RB_46


title: mcm23Apol32D BrdU 25C 30' sonication add S.pombe spike in rep1 [Alb935_merge]

description: add S.pombe spike in


title: IgG4-RD3

description: 10x Genomics

value: male


title: D203_LLN_TCRAD


title: RB_44


title: mcm23Apol32D Input 25C 30' MNase add S.pombe spike in rep2 [Alb894_mcm23Apol32D_Input_S30]

description: add S.pombe spike in

value: 25C 30' MNase

value: Input


title: IgG4-RD2

description: 10x Genomics


title: COV060_Blood_TCRG

source_name: Blood

value: Blood

value: pediatric


title: mcm23Apol32D Input 25C 30' MNase add S.pombe spike in rep1 [Alb832_mcm23Apol32D_Input_S30]

description: add S.pombe spike in


title: RB_43

value: retinoblastoma

value: A


title: mcm23Apol32D BrdU 25C 30' MNase add S.pombe spike in rep2 [Alb909_mcm23Apol32D_BrdU_S30]

description: add S.pombe spike in

value: BrdU


title: IgG4-RD1

description: 10x Genomics

value: retroperitoneum tissue


title: COV060_Blood_TCRAD


title: RB_42


title: 97H_KDM1A_shZMYM3_H3K4me1_CUTTAG

first: Boshi

last: Wang

address: No.800 Dongchuan Road

institute: Shanghai Cancer Institute

data_processing:
The sequencing reads obtained from the Illumina platform were subjected to quality control using FastQC (v0.11.9) to assess the quality of the reads.
Adapter trimming and read filtering were performed using Trim-galore (0.6.5-1).
The filtered reads were then aligned to the human genome (UCSC hg38) using Bowtie2 version 2.2.6.
The aligned reads were processed by MACS2 (v2.2.7.1) to call peaks and transformed to bigwig formatted files by bamCoverage function in Deeptools (v3.5.1) with default parameters.
Assembly: hg38
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

source_name: liver

extract_protocol:
The CUT&Tag experiments were performed using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme Biotech Co., Ltd., TD903) according to the manufacturer’s instructions.
The library was constructed by TruePrep® Index Kit V2 for Illumina kit and PCR amplification

value: liver

value: HCC

tag: cut&tag antibody

value: H3K4me1 ab176877 Abcam


title: mcm23Apol32D BrdU 25C 30' MNase add S.pombe spike in rep1 [Alb936_merge]

description: add S.pombe spike in

tag: genotype


title: RB_41


title: 97H_KDM1A_shcon_H3K4me1_CUTTAG


title: mcm23Apol3pip Input 25C 30' sonication add S.pombe spike in rep2 [Alb895_mcm23Apol3pip_Input_S30]

description: add S.pombe spike in

tag: batch

value: 25C 30' sonication


title: mcm23Apol3pip Input 25C 30' sonication add S.pombe spike in rep1 [Alb833_mcm23Apol3pip_Input_S30]

description: add S.pombe spike in


title: COV053_Blood_TCRAD

value: gd T cells

value: unknown


title: RB_33


title: 97H_V_shcon_H3K4me1_CUTTAG

tag: cell line

value: vector+shcontrol


title: HepG2_shKDM1A_2_RNAseq

data_processing:
Raw RNA-seq data were subjected to quality control using FastQC (v0.11.9) and trimmed using Trim_galore (0.6.5-1).
SortMeRNA (4.2.0) was used to remove rRNA reads to generate clean data.
The clean reads were aligned to the human reference genome (hg38) using the HISAT2 (version 2.2.1) aligner to generate BAM files.
The aligned reads (BAM files) were transformed into bigwig files using Deeptools software (v3.5.1)
Assembly: hg38
Supplementary files format and content: bigwig

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Life Technologies, CA, USA) according to the manufacturer's protocol, and RNA integrity was assessed using an Agilent Bioanalyzer 2100 (Agilent Technologies, CA, USA) to obtain RIN values. RNA with RIN values > 7 was purified using an RNAClean XP Kit (Beckman Coulter, Inc. CA, USA) and RNase-Free DNase Set (QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using a VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme, Nanjing, China), and sequencing was performed on an Illumina HiSeq 2500 system.


title: RB_28


title: mcm23Apol3pip BrdU 25C 30' sonication add S.pombe spike in rep2 [Alb910_mcm23Apol3pip_BrdU_S30]

description: add S.pombe spike in

tag: strain


title: RB_26


title: mcm23Apol3pip BrdU 25C 30' sonication add S.pombe spike in rep1 [Alb845_mcm23Apol3pip_BrdU_S30]

description: add S.pombe spike in

tag: condition


title: AUD207_Blood_TCRAD

tag: tissue


title: HepG2_shKDM1A_1_RNAseq

tag: treatment


title: AUD205_Blood_TCRG


title: RB_24


title: mcm23Apol3pip Input 25C 30' MNase add S.pombe spike in rep2 [Alb896_mcm23Apol3pip_Input_S30]

description: add S.pombe spike in


title: HepG2_shctr_RNAseq

value: sh-control


title: AUD205_Blood_TCRAD


title: HepG2_KDM1A_CUTTAG

value: WT

value: KDM1A ab129195 Abcam


title: AUD194_Blood_TCRG


title: COV053_Blood_TCRG


title: RB_22


title: HepG2_shKDM1A_H3K27ac_CUTTAG

value: KDM1A shRNA

value: H3K27ac ab4729 Abcam


title: mcm23Apol3pip BrdU 25C 30' MNase add S.pombe spike in rep2 [Alb911_mcm23Apol3pip_BrdU_S30]

description: add S.pombe spike in

value: 25C 30' MNase


title: mcm23Apol3pip Input 25C 30' MNase add S.pombe spike in rep1 [Alb834_mcm23Apol3pip_Input_S30]

description: add S.pombe spike in

value: Input


title: RB_35

value: retinoblastoma

value: A


title: RB_23


title: AUD207_Blood_TCRG

value: Blood

value: pediatric


title: AUD194_Blood_TCRAD


title: RB_21

value: B


title: AUD192_Blood_TCRG


title: HepG2_shctr_H3K27ac_CUTTAG

value: liver

value: HCC

value: control shRNA


title: pol3079 input 25C 30' sonication add S.pombe spike in rep3 [Alb1039_pol3079_input_S30]

description: add S.pombe spike in

value: 25C 30' sonication

value: input


title: RB_20


title: mcm23Apol3pip BrdU 25C 30' MNase add S.pombe spike in rep1 [Alb846_mcm23Apol3pip_BrdU_S30]

description: add S.pombe spike in

value: BrdU


title: pol3079 input 25C 30' sonication add S.pombe spike in rep2 [Alb1015_pol3079_input_S30]

description: add S.pombe spike in


title: AUD192_Blood_TCRAD

value: gd T cells


title: AUD190_Blood_TCRG


title: pol3079 input 25C 30' sonication add S.pombe spike in rep1 [Alb969_pol3079_input_S30]

description: add S.pombe spike in


title: AUD190_Blood_TCRAD


title: HepG2_shKDM1A_H3K4me2_CUTTAG

value: H3K4me2 ab32356 Abcam


title: HepG2_shctr_H3K4me2_CUTTAG


title: pol3079 BrdU 25C 30' sonication add S.pombe spike in rep3 [Alb1047_pol3079_BrdU_S30]

description: add S.pombe spike in


title: AUD182_Blood_TCRG


title: pol3079 BrdU 25C 30' sonication add S.pombe spike in rep2 [Alb1027_pol3079_BrdU_S30]

description: add S.pombe spike in


title: AUD182_Blood_TCRAD


title: HepG2_shctr_H3K4me1_CUTTAG

value: H3K4me1 ab176877 Abcam


title: pol3079 BrdU 25C 30' sonication add S.pombe spike in rep1 [Alb979_pol3079_BrdU_S30]

description: add S.pombe spike in


title: pol3079 input 25C 30' MNase add S.pombe spike in rep3 [Alb1040_pol3079_input_S30]

description: add S.pombe spike in


title: 97H_KDM1A_shZMYM3_KDM1A_CUTTAG

value: KDM1A ab129195 Abcam


title: HepG2_shctr_H3K9me2_CUTTAG

value: H3K9me2 ab1220 Abcam


title: AUD181_Blood_TCRAD


title: pol3079 input 25C 30' MNase add S.pombe spike in rep2 [Alb1016_pol3079_input_S30]

description: add S.pombe spike in

value: 25C 30' MNase


title: SET1-3HA_ard1Δ-2-HA

city: Chuncheon

first: Junsoo

last: Oh

country: South Korea

institute: Kangwon National University

data_processing:
The sequencing adapter removal and quality-based trimming on raw data was performed by Trimmomatic v. 0.36 with TruSeq adapter sequences.
Cleaned reads were mapped to reference genome using bowtie v2.4.2 with default parameter
For normalization, S. pombe spike-in reads in each sample was calculated.
We assumed that the amount of spike-in added to each sample is same, and the normalization ratio was calculated as "1000000/spike-in reads" for each sample.
The normalized bedGraph was produced by using 'bamCoverage --scaleFactor' and calculated normalization ratio.
BedGraph files were converted to BigWig files and the resulted bw files were averaged by WiggleTools 1.2 (https://github.com/Ensembl/WiggleTools).
Assembly: Saccharomyces cerevisiae S288C genome assembly R64 (sacCer3)
Supplementary files format and content: bigwig

source_name: Yeast cell

growth_protocol: TAP-tagged strains and HA-tagged strains (and their cognate notag controls) were grown in 200ml of YPD (Yeast extract Peptone Dextrose; 1% Yeast Extract, 2% Peptone, 2% Dextrose (Glucose)) at 30℃ until OD600 was 0.5-0.6 and 1.0, respectively

extract_protocol:
Cells were harvested and immediately crosslinked. Then, cells were sonicated and proteins of interest were immunoprecipitated by antibodies.
Libraries were prepared with NEBNext ChIP-Seq Library Kit following the manufacturer’s instruction.

value: Yeast cell

tag: chip antibody

value: Anti-HA (Santacruz, sc-7692)

value: SET1-3HA set1delta (JL1205)

value: SET1-3HA in ard1 deletion


title: 97H_KDM1A_shcon_KDM1A_CUTTAG


title: pol3079 input 25C 30' MNase add S.pombe spike in rep1 [Alb970_pol3079_input_S30]

description: add S.pombe spike in


title: p59_ms_tim1

city: Boston

first: Shannan

last: Ho Sui

address: 401 Park Drive

institute: Harvard

data_processing:
bcbio-nextgen bulk RNA-seq pipeline (version 1.2.8-1c563f1)
Assembly: hg38
Supplementary files format and content: TPM counts from Salmon aggregated at the gene level by tximport

source_name: Peripheral blood

extract_protocol:
Trombetta Protocol
Nextera XT

value: Peripheral blood

value: TIM-1+ memory B (TIM-1+ TIGIT-) cells

tag: patient


title: 97H_V_shcon_KDM1A_CUTTAG

value: liver

tag: cell type

value: HCC

value: vector+shcontrol


title: p55_ms_tim1


title: HepG2_shKDM1A_H3K4me1_CUTTAG

value: KDM1A shRNA


title: SET1-3HA_ard1Δ-1-HA


title: pol3079 BrdU 25C 30' MNase add S.pombe spike in rep3 [Alb1048_pol3079_BrdU_S30]

description: add S.pombe spike in

value: BrdU


title: SET1-3HA-2-HA

value: SET1-3HA in FM392 (JL347)


title: HepG2_shKDM1A_H3K9me2_CUTTAG


title: p53_ms_tim1


title: AUD181_Blood_TCRG

city: New York City

value: Blood

value: gd T cells

tag: developmental stage

value: pediatric


title: SUM159PT from in vivo xenograft, tumor 5

city: Milano

first: Francesco

last: Nicassio

address: Via Adamello 16

department: Center for genomic science

country: Italy

institute: Istituto Italiano di Tecnologia

data_processing:
Reads were trimmed, filtered and aligned using STAR (2.7.3).
Read count extraction and TPM normalization were performed using FeatureCounts.
The signature of  differentially expressed genes (DEGs) was defined using DESeq2
Assembly: HG38
Supplementary files format and content: txt file containing the DEGs called by DESeq2 analysis of Tumors (N=5) vs 2D cells (N=6)

source_name: breast

growth_protocol: For in vivo xenografts, SUM159PT cells (100k) were resuspended in a mix of 14 ul PBS amd 6 ul Matrigel and implanted in the fourth inguinal mammary gland of 10-week-old animals. Tumors were collected when they reached 1.2 cm on the largest diamater.

extract_protocol:
Tumors were resected, digested with mechanical (gentleMACS) and enzymatic (collagenase, hyaluronidase) methods, filtered and depleted from mouse and dead cells. RNA was harvested using Maxwell RSC miRNA Tissue Kit according to the manufacturer’s protocol.
Libraries for RNA-seq were prepared from 1 ug of total RNA using Truseq Total RNA Library Prep Kit (Illumina) following manufacturer's protocols.

value: breast

value: female

tag: time

value: day 30

value: from in vivo xenograft


title: pol3079 BrdU 25C 30' MNase add S.pombe spike in rep2 [Alb1028_pol3079_BrdU_S30]

description: add S.pombe spike in

value: 25C 30' MNase


title: SUM159PT from in vivo xenograft, tumor 4


title: SET1-3HA-1-HA

value: Yeast cell

value: Anti-HA (Santacruz, sc-7692)


title: p51_ms_tim1

value: Peripheral blood

value: TIM-1+ memory B (TIM-1+ TIGIT-) cells


title: SUM159PT from in vivo xenograft, tumor 3


title: pol3079 BrdU 25C 30' MNase add S.pombe spike in rep1 [Alb980_pol3079_BrdU_S30]

description: add S.pombe spike in


title: control_case_1

type: RNA

city: Amol

first: Hossein

last: Azizi

address: Taleghani str, Abouzar

country: Iran

institute: Amol University of Special Modern Technologies

description: Gene expression of control 1

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 50683 array features.

data_processing: Normalization and biostatistical analysis were performed by MicroDiscovery GmbH of Berlin, Germany.

source_name: Semen of control case 1

label_protocol: Cy3-labelled cRNA

extract_protocol: Isolation of sperm RNA from sperm samples was performed according to manufacturer's instructions using Trizol RNA isolation reagent (Gibco BRL, Grand Island, USA). Compared to normal sperm motility and sperm motility affected individuals, ejaculated sperm from ten healthy individuals was examined. Using gel electrophoresis and UV spectrophotometry, RNA preparations were assessed for quality and quantity.

value: testis

tag: gender

value: male

tag: age

value: control


title: azoospermia_case_3

description: Gene expression of non-obstructive azoospermia case 3

source_name: Semen of azoospermia case 3

value: azoospermia


title: Notag-HA

value: Wildtype (FM392)


title: control_case_3

description: Gene expression of control 3

source_name: Semen of control case 3


title: azoospermia_case_2

description: Gene expression of non-obstructive azoospermia case 2

source_name: Semen of azoospermia case 2


title: control_case_2

description: Gene expression of control 2

source_name: Semen of control case 2


title: azoospermia_case_1

description: Gene expression of non-obstructive azoospermia case 1

source_name: Semen of azoospermia case 1


title: p46_ms_tim1


title: pol322A2 input 25C 30' sonication add S.pombe spike in rep2 [Alb1019_pol322A2_input_S30]

description: add S.pombe spike in

value: 25C 30' sonication

value: input


title: p47_ms_tim1


title: YTK1788-2-TAP

value: IgG Sepharose (GE healthcare 17-0969-01)

value: SET1-TAP in ard1 deletion


title: SUM159PT from in vivo xenograft, tumor 2

value: breast

value: female


title: p44_ms_tim1


title: pol322A2 input 25C 30' sonication add S.pombe spike in rep1 [Alb973_pol322A2_input_S30]

description: add S.pombe spike in


title: YTK1788-1-TAP


title: SUM159PT untreated, day 15, replicate 3

value: day 15

value: untreated


title: pol322A2 BrdU 25C 30' sonication add S.pombe spike in rep2 [Alb1031_pol322A2_BrdU_S30]

description: add S.pombe spike in

value: BrdU


title: p42_ms_tim1


title: YF664-2-TAP

value: Yeast cell


title: pol322A2 BrdU 25C 30' sonication add S.pombe spike in rep1 [Alb983_pol322A2_BrdU_S30]

description: add S.pombe spike in


title: p20_ms_tim1

value: Peripheral blood


title: SUM159PT untreated, day 15, replicate 2


title: YF664-1-TAP


title: SUM159PT untreated, day 15, replicate 1


title: p16_ms_tim1

value: TIM-1+ memory B (TIM-1+ TIGIT-) cells


title: pol322A2 input 25C 30' MNase add S.pombe spike in rep2 [Alb1020_pol322A2_input_S30]

description: add S.pombe spike in

value: 25C 30' MNase


title: SUM159PT from in vivo xenograft, tumor 1

value: day 30

value: from in vivo xenograft


title: p38_ms_tim1


title: SUM159PT untreated, day 0, replicate 2

value: day 0


title: F1 (B6 mother and MSM father), replicate #1

city: Nagoya

first: Kenji

last: Ichiyanagi

address: Furo-cho, Chikusa-ku

department: Graduate School of Bioagricultural Sciences

institute: Nagoya University

data_processing:
Trim Galore! (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was used to perform adapter trimming on the mRNA-Seq reads using the options, -q 30 --length 30 --paired --three_prime_clip_R1 1 three_prime_clip_R2 2.
Read alignment was done using Tophat2 with masked mm10 as the reference genome (wherein the nucleotides at SNP sites were changed to N), using alignment options, -G --library-type fr-firststrand -g 1.
SNPsplit was used to discriminate the B6 and MSM alleles from the aligned reads based on known SNP positions.
The allele frequencies (the number of B6-derived reads divided by the total of B6- and MSM-derived reads) for each gene were calculated using a Perl script.
Assembly: mm10, but the nucleotides at SNP sites were changed to N
Supplementary files format and content: tab-divided text file showing gene name, expression level in FPKM, and allele frequency for B6.

molecule: polyA RNA

extract_protocol:
Liver was homogenized in Isogen, RNA was purified using DirectZol RNA micro prep kit.
NEBNext poly(A) mRNA magnetic isolation module and NEBNext Ultra directional mRNA library preparation kit were used for library preparation.

value: liver

value: 5 months old

tag: cross

value: BM


title: p37_ms_tim1


title: F1 (B6 mother and MSM father), replicate #2

tag: Sex


title: YF336-TAP

value: IgG Sepharose (GE healthcare 17-0969-01)

value: Wildtype (BY4741)


title: SUM159PT untreated, day 0, replicate 3

value: breast


title: SUM159PT untreated, day 0, replicate 1

value: female


title: F1 (MSM mother and B6 father), replicate #2

value: MB


title: pol322A2 BrdU 25C 30' MNase add S.pombe spike in rep2 [Alb1032_pol322A2_BrdU_S30]

description: add S.pombe spike in


title: p35_hc_tim1


title: pol322A2 BrdU 25C 30' MNase add S.pombe spike in rep1 [Alb984_pol322A2_BrdU_S30]

description: add S.pombe spike in


title: p36_ms_tim1


title: F1 (MSM mother and B6 father), replicate #1


title: pol32D Input 25C 30' sonication add S.pombe spike in rep2 [Alb889_pol32D_Input_S30]

description: add S.pombe spike in

value: 25C 30' sonication

value: Input


title: SUM159PT cells_bulk sorted and propagated for 19 passages_replicate1

data_processing:
HTS-FLOW v2
Sequence reads were trimmed for adaptor sequence/low-quality sequence
Trimmed sequence reads were mapped to hg38  using STAR
Read count extraction and TPM normalization were performed using FeatureCounts; DEGs were called using EdgeR within Galaxy (Galaxy Version 3.36,0)
Assembly: hg38
Supplementary files format and content: TM4SF1_GEX_counts.txt: tab delimited file that includes raw count values for all genes (Sorted samples: input of EdgeR)
Supplementary files format and content: edgeR_TM4SF1_high-BULK.tsv: EdgeR output files containing L2FC and FDR for TM4SF1 high vs bulk samples at Sorting
Supplementary files format and content: TPM_counts.txt: tab delimited file that includes TPM for all genes in all samples (Sort, P4, P19)

extract_protocol:
RNA was harvested using Maxwell RSC miRNA Tissue Kit according to the manufacturer’s protocol.. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Truseq Total RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: SUM159 were stained with an anti-TM4SF1-APC antibody (miltenyi) and sorted using Fusion Aria Sorter. The top 5% TM4SF1 cells were gated as "high".

value: untreated


title: pol32D Input 25C 30' sonication add S.pombe spike in rep1 [Alb827_pol32D_Input_S30]

description: add S.pombe spike in


title: SUM159PT cells_bulk sorted and propagated for 19 passages_replicate2


title: p33_hc_tim1

value: Peripheral blood


title: SUM159PT cells_sorted for TM4SF1_high and propagated for 19 passages_replicate2


title: pol32D BrdU 25C 30' sonication add S.pombe spike in rep2 [Alb902_pol32D_BrdU_S30]

description: add S.pombe spike in

value: BrdU


title: p32_hc_tim1

value: TIM-1+ memory B (TIM-1+ TIGIT-) cells


title: BMMCs, si12A+C, 3

city: Bellinzona

first: Cristina

last: Leoni

address: Via F. Chiesa 5

institute: Institute for Research in Biomedicine

description: NanoString nCounter Myeloid Innate Immunity Panel

hyb_protocol: Samples were hybridized for 16h at 65°C

scan_protocol: Samples were ran on a Nanostring Sprint Profiler

data_processing: Raw data was filtered for genes with counts value of >50 and processed with batch correction using the Omics Playground platform.

label: not provided

source_name: BMMCs transfected with siRNAs against Zc3h12a and Zc3h12c, stimulated with IgE-antigen complexes for 2h

label_protocol: 50ng of total RNA were labelled with the nCounter Myeloid Innate Immunity Panel codeset according to manufacturers protocol

growth_protocol: Total bone marrow was isolated from mouse and cultured in humidified atmosphere with 5% CO2 at 37C for at least 4 weeks in the presence of IL-3 to induce bone marrow-derived mast cell (BMMC) differentiation. BMMCs were transfected with siRNAs and cultured for 48 hours.

extract_protocol: Cells were resuspended in Trizol and total RNA was extracted with Direct-Zol RNA mini Prep (Zymo Research)

treatment_protocol: Cells were activated IgE and antigen complexes for 2h.

value: bone marrow-derived mast cells

value: 2h IgE-antigen stimulation

tag: sirna-targeted gene/s

value: Zc3h12a and Zc3h12c

tag: sample type

value: test


title: SUM159PT cells_sorted for TM4SF1_high and propagated for 19 passages_replicate1


title: BMMCs, si12C, 3

source_name: BMMCs transfected with siRNAs against Zc3h12c, stimulated with IgE-antigen complexes for 2h


title: p34_hc_tim1


title: pol32D BrdU 25C 30' sonication add S.pombe spike in rep1 [Alb934_merge]

description: add S.pombe spike in

tag: batch

tag: genotype


title: pol322A2 input 25C 30' MNase add S.pombe spike in rep1 [Alb974_pol322A2_input_S30]

description: add S.pombe spike in

tag: strain

value: 25C 30' MNase

value: input


title: SUM159PT cells_bulk sorted and propagated for four passages_replicate2

tag: cell line


title: p31_hc_tim1

tag: tissue


title: SUM159PT cells_sorted for TM4SF1_high and propagated for four passages_replicate2

tag: treatment


title: pol32D BrdU 25C 30' MNase add S.pombe spike in rep2 [Alb903_pol32D_BrdU_S30]

description: add S.pombe spike in

tag: condition


title: pol32D Input 25C 30' MNase add S.pombe spike in rep1 [Alb828_pol32D_Input_S30]

description: add S.pombe spike in


title: p30_hc_tim1

tag: patient


title: BMMCs, siGLO, 3

source_name: BMMCs transfected with non-targeting siGLO, stimulated with IgE-antigen complexes for 2h

tag: cell type

value: control


title: BMMCs, si12A, 3

source_name: BMMCs transfected with siRNAs against Zc3h12a, stimulated with IgE-antigen complexes for 2h